gebhart/patrepeval huggingface dataset:
Structural Analysis of the Hepatitis C Virus RNA Polymerase in Complex with Ribonucleotides (2002)

We report here the results of a systematic high-resolution X-ray crystallographic analysis of complexes of the hepatitis C virus (HCV) RNA polymerase with ribonucleoside triphosphates (rNTPs) and divalent metal ions. An unexpected observation revealed by this study is the existence of a specific rGTP binding site in a shallow pocket at the molecular surface of the enzyme, 30 A away from the catalytic site. This previously unidentified rGTP pocket, which lies at the interface between fingers and thumb, may be an allosteric regulatory site and could play a role in allowing alternative interactions between the two domains during a possible conformational change of the enzyme required for efficient initiation. The electron density map at 1.7-A resolution clearly shows the mode of binding of the guanosine moiety to the enzyme. In the catalytic site, density corresponding to the triphosphates of nucleotides bound to the catalytic metals was apparent in each complex with nucleotides. Moreover, a network of triphosphate densities was detected; these densities superpose to the corresponding moieties of the nucleotides observed in the initiation complex reported for the polymerase of bacteriophage phi6, strengthening the proposal that the two enzymes initiate replication de novo by similar mechanisms. No equivalent of the protein stacking platform observed for the priming nucleotide in the phi6 enzyme is present in HCV polymerase, however, again suggesting that a change in conformation of the thumb domain takes place upon template binding to allow for efficient de novo initiation of RNA synthesis.
Electrolytic Effects During Tissue Ablation by Electroporation (2015)

Nonthermal irreversible electroporation is a new tissue ablation technique that consists of applying pulsed electric fields across cells to induce cell death by creating permanent defects in the cell membrane. Nonthermal irreversible electroporation is of interest because it allows treatment near sensitive tissue structures such as blood vessels and nerves. Two recent articles report that electrolytic reaction products at electrodes can be combined with electroporation pulses to augment and optimize tissue ablation. Those articles triggered a concern that the results of earlier studies on nonthermal irreversible electroporation may have been tainted by unaccounted for electrolytic effects. The goal of this study was to reexamine previous studies on nonthermal irreversible electroporation in the context of these articles. The study shows that the results from some of the earlier studies on nonthermal irreversible electroporation were affected by unaccounted for electrolysis, in particular the research with cells in cuvettes. It also shows that tissue ablation ascribed in the past to irreversible electroporation is actually caused by at least 3 different cytotoxic effects: irreversible electroporation without electrolysis, irreversible electroporation combined with electrolysis, and reversible electroporation combined with electrolysis. These different mechanisms may affect cell and tissue ablation in different ways, and the effects may depend on various clinical parameters such as the polarity of the electrodes, the charge delivered (voltage, number, and length of pulses), and the distance of the target tissue from the electrodes. Current clinical protocols employ ever-increasing numbers of electroporation pulses to values that are now an order of magnitude larger than those used in our first fundamental nonthermal irreversible electroporation studies in tissues. The different mechanisms of cell death, and the effect of the clinical parameters on the mechanisms may explain discrepancies between results of different clinical studies and should be taken into consideration in the design of optimal electroporation ablation protocols.
Electrogenerated chemiluminescence. 37. Aqueous ecl systems based on tris(2,2'-bipyridine)ruthenium(2+) and oxalate or organic acids (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrogenerated chemiluminescence. 37. Aqueous ecl systems based on tris(2,2'-bipyridine)ruthenium(2+) and oxalate or organic acidsIsrael Rubinstein and Allen J. BardCite this: J. Am. Chem. Soc. 1981, 103, 3, 512–516Publication Date (Print):February 1, 1981Publication History Published online1 May 2002Published inissue 1 February 1981https://pubs.acs.org/doi/10.1021/ja00393a006https://doi.org/10.1021/ja00393a006research-articleACS PublicationsRequest reuse permissionsArticle Views2643Altmetric-Citations452LEARN 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
(R)‐Lactyl‐CoA dehydratase from Clostridium propionicum (1992)

1. A new two-step method for purifying component E II of lactyl-CoA dehydratase was developed. The source of the enzyme was Clostridium propionicum grown on either D,L-alanine or L-threonine. No difference in these preparations was observed whether during purification or by SDS/PAGE of the pure enzymes. Both preparations exhibited similar activities towards (R)-lactyl-CoA as well as towards (R)-2-hydroxybutyryl-CoA, the latter being the superior substrate. 2. Three species of (2R)-2-hydroxybutyrate labelled with 3H at C3 were prepared containing 96%, 37% and 63% of the 3H in the 3S-position. By incubation of these species with acetyl-CoA, propionate CoA-transferase and lactyl-CoA dehydratase 104%, 32% and 70% of the 3H, respectively, was release as 3HOH. The data indicate that stereospecific abstraction of the 3Si hydrogen of (2R)-2-hydroxybutyryl-CoA during the dehydration. 3. The identity of the product of the dehydration as crotonyl-CoA was established by the combined action of the enzymes crotonase and (S)-3-hydroxyacyl-CoA dehydrogenase. The results indicate that the elimination of water from (R)-2-hydroxybutyryl-CoA occurs in a syn mode. 4. All enzyme activities necessary for the conversion of L-threonine via (R)-2-hydroxybutyryl-CoA to butyrate were detected in cell-free extracts of C. propionicum. 5. A new mechanism for the dehydration of lactyl-CoA is proposed.
Current Concepts Review: Hallux Valgus Part II: Operative Treatment (2007)

Outcome Studies for Hallux Valgus Results of most hallux valgus corrective procedures typically focus on the physicians’ perceptions rather than the patients’ perceptions of outcome.113 Thordarson et al.113 noted that patients’ perceptions of outcome generally are reduced to satisfied, satisfied with reservations, or dissatisfied. Although the American Orthopaedic Foot and Ankle Society (AOFAS) rating system aims to standardize outcomes data collection,55 it remains a physician-driven tool. Furthermore, its validity has been questioned in the evaluation of the hindfoot,118 a shortcoming that may also manifest in the forefoot.9 This is not a shortcoming isolated to the AOFAS rating system. In a recent meta-analysis of outcomes scales in foot and ankle surgery, Button and Pinney12 concluded that none of the 49 rating scales identified proved to be reliable, valid, or responsive in patients with foot and ankle conditions. The effort by a team of AOFAS members to create such an outcomes tool suggests that the AOFAS clinical rating system lacks adequate assessment of quality of life measures.114 Recently, SooHoo et al.110 demonstrated increased responsiveness of foot and ankle specific outcomes tools compared to the SF-36. However, the level of responsiveness for the bodily pain subscale and the physical component summary approached that of the AOFAS outcomes
Formation of Glutaric and Adipic Acids from n-Alkanes with Odd and Even Numbers of Carbons by Candida tropicalis OH23 (1971)

Many strains of yeast which can utilize n-alkanes as the sole source of carbon were isolated from flowers and fruits. Among them, a strain, OH23, identified as Candida tropicalis, formed acidic substances from n-alkanes. The principal products from n-alkanes with odd and even numbers of carbons were identified as glutaric and adipic acids, re spectively. The culture conditions for their formation were investigated.
Structure of amplified normal and variant dihydrofolate reductase genes in mouse sarcoma S180 cells. (1982)

We constructed a gene library from a murine cell line with amplified dihydrofolate reductase (dhfr) genes by inserting random segments of DNA into lambda Ch4A. From this library, the dhfr gene and 30 kilobase pairs of surrounding DNA were cloned, and the restriction map was determined. All of the coding regions were sequenced and show that the gene spans a total of 31 kilobase pairs and has five intervening sequences in the coding portion of the gene. In addition, two classes of variant dhfr genes were found in the amplified line, which were amplified and present at levels of 10 to 30% of the normal dhfr genes. Numerous repeated sequences were located throughout the gene region, some of which share homology with previously defied families of repeats.
Relationship of M protein genes in group A streptococci. (1985)

The M protein of group A streptococci is considered one of the primary virulence determinants of this organism because it prevents phagocytosis. All of the 56 different M protein types of group A streptococci tested contain a DNA region that hybridizes with a labeled probe consisting of DNA encoding the type 6 M protein (emm6 gene). In addition, 2 of 3 functionally M- group A strains (strains that are successfully phagocytized) also contain this gene, but this DNA is not present in 1 M- strain. Of the other streptococcal groups, only groups C and G, which are closely related to group A, contain DNA that hybridizes with emm6. None of the non-streptococcal Gram-positive bacteria tested contains emm6-related DNA. In the strain from which emm6 was cloned, there appears to be only a single copy of this gene.
The division of household work during the transition to parenthood (1987)

Abstract This article explores the impact of parenthood on the gender division of the household workload, including employment, housework and childcare. A British sample, originally consisting of 96 couples, were interviewed on several occasions during pregnancy and the first postnatal year. The results illustrate how the transition period emphasizes ‘traditional’ patterns in the division of household work. There were no consistent class differences in male participation in housework and childcare, though working-class men had longer hours in employent. Parents' ‘ideal’ work-home arrangements and indicators of maternal dissatisfaction with their position suggest that the division of workload evolving after birth is not generally preferred.
Estimating T-cell repertoire diversity: limitations of classical estimators and a new approach (2015)

A highly diverse T-cell receptor (TCR) repertoire is a fundamental property of an effective immune system, and is associated with efficient control of viral infections and other pathogens. However, direct measurement of total TCR diversity is impossible. The diversity is high and the frequency distribution of individual TCRs is heavily skewed; the diversity therefore cannot be captured in a blood sample. Consequently, estimators of the total number of TCR clonotypes that are present in the individual, in addition to those observed, are essential. This is analogous to the 'unseen species problem' in ecology. We review the diversity (species richness) estimators that have been applied to T-cell repertoires and the methods used to validate these estimators. We show that existing approaches have significant shortcomings, and frequently underestimate true TCR diversity. We highlight our recently developed estimator, DivE, which can accurately estimate diversity across a range of immunological and biological systems.
A Molecular Genetic Intervention for AIDS—Effects of a Transdominant Negative Form of Rev. Hughes Medical Institute Research Laboratories, Ann Arbor, Michigan (1994)

16.0 Scientific Abstract The HIV-1 Rev protein is encoded by a fully spliced viral mRNA synthesized early in virus infection and required for productive HIV replication (23). Rev facilitates the cytoplasmic appearance of unspliced viral mRNAs and plays a role in the regulation of virus latency (24,25). Mutations in a well-conserved leucine rich domain of Rev give rise to a defective protein that acts as a transdominant inhibitor of HIV replication, which could provide a potential anti-HIV therapy. In this study, we will evaluate the efficacy of intracellular inhibition of HIV infection with a mutant form of Rev, M10. We will introduce the rev M10 gene into peripheral blood CD4+ T cells. CD4+ cells will be genetically modified in patients using either (a.) a retroviral vector or (b.) a non-viral vector. In each case, a control vector identical to the Rev M10 expression vector but with a frameshift that inactivates gene expression will be used to transduce a parallel population of CD4+ cells. These cells will be returned to the patient, and the survival of the cells in each group compared by limiting dilution PCR. In this way, we will determine whether Rev M10 can prolong the survival of CD4+ cells in AIDS patients, thus conferring protection against HIV infection.
Elevated Levels of Apoptosis Regulator Proteins P53 and BCL-2 are Independent Prognostic Biomarkers in Surgically Treated Clinically Localized Prostate Cancer (1996)

p53 and bcl-2 appear to be important biomarkers that predict recurrence in clinically localized PC after RP.
Activation of cyclin D1-related kinase in human lung adenocarcinoma (1999)

Cyclin D1 gene amplification is an important event in many cancers, but it is rarely found in non-small-cell lung cancer (NSCLC). This study was conducted in an attempt to clarify any other mechanisms related to cyclin D1 involvement in the malignant transformation of NSCLC, and we clearly showed for the first time that cyclin D1-related kinases are activated in NSCLC, especially in adenocarcinoma but not in squamous cell carcinoma. The results of this study strongly suggest that enhanced cyclin D1-related kinase activity could contribute to a progression of adenocarcinoma in NSCLC.
A search engine for 3D models (2003)

As the number of 3D models available on the Web grows, there is an increasing need for a search engine to help people find them. Unfortunately, traditional text-based search techniques are not always effective for 3D data. In this article, we investigate new shape-based search methods. The key challenges are to develop query methods simple enough for novice users and matching algorithms robust enough to work for arbitrary polygonal models. We present a Web-based search engine system that supports queries based on 3D sketches, 2D sketches, 3D models, and/or text keywords. For the shape-based queries, we have developed a new matching algorithm that uses spherical harmonics to compute discriminating similarity measures without requiring repair of model degeneracies or alignment of orientations. It provides 46 to 245% better performance than related shape-matching methods during precision--recall experiments, and it is fast enough to return query results from a repository of 20,000 models in under a second. The net result is a growing interactive index of 3D models available on the Web (i.e., a Google for 3D models).
Low-Rank Approximations for Conditional Feedforward Computation in Deep Neural Networks (2013)

Scalability properties of deep neural networks raise key research questions, particularly as the problems considered become larger and more challenging. This paper expands on the idea of conditional computation introduced by Bengio, et. al., where the nodes of a deep network are augmented by a set of gating units that determine when a node should be calculated. By factorizing the weight matrix into a low-rank approximation, an estimation of the sign of the pre-nonlinearity activation can be efficiently obtained. For networks using rectified-linear hidden units, this implies that the computation of a hidden unit with an estimated negative pre-nonlinearity can be ommitted altogether, as its value will become zero when nonlinearity is applied. For sparse neural networks, this can result in considerable speed gains. Experimental results using the MNIST and SVHN data sets with a fully-connected deep neural network demonstrate the performance robustness of the proposed scheme with respect to the error introduced by the conditional computation process.
Color image-adaptive watermarking (2003)

A novel scheme for the watermarking of colour images is presented in this communication. The first objective is to find the most suitable alternative to RGB color space, which is highly correlated. Colour spaces with linear relation to RGB colour space with uncorrelated components are found to be most suitable for watermarking applications. Second objective is to make the scheme adaptive to o/spl circ/c$80a/spl ring/ colour image. This is achieved by keeping the PSNR in a predefined quality range, while timing the watermark strength parameter. Watermark detection is fast and blind, i.e. only the watermark generation and coefficient randomization keys are needed, and not the original image. The presented results demonstrate the robustness of the method against some common image processing attacks such as compression, scaling, uniform or gaussian noise addition, median filtering, cropping and multiple watermarking.
Movement Primitives, Principal Component Analysis, and the Efficient Generation of Natural Motions (2005)

We propose a framework for robot movement coordination and learning that combines elements of movement storage, dynamic models, and optimization, with the ultimate objective of efficiently generating natural, human-like motions. One of the novel features of our approach is that each movement primitive is represented and stored as a set of joint trajectory basis functions; these basis functions are extracted via a principal component analysis of human motion capture data. By representing arbitrary movements as a linear combination of these basis functions, and by taking advantage of recently developed geometric optimization algorithms for multibody systems, dynamics-based optimization can be more efficiently performed. Case studies with a diverse set of arm movements demonstrate the feasibility of our approach.
A synthetic peptide from myelin proteolipid protein induces experimental allergic encephalomyelitis. (1988)

Immunization of animals with proteolipid protein, the major protein constituent of central nervous system myelin, produces experimental allergic encephalomyelitis. The goal of the present study was to identify an encephalitogenic determinant of this protein. For this purpose, SWR mice were immunized with five groups of pooled synthetic peptides corresponding to various regions of the myelin proteolipid protein sequence. Clinical EAE was observed in only one group. Inguinal lymph node cells from animals in this group responded ([3H]thymidine incorporation) to a peptide within the pool containing residues 103-116 YKTTICGKGLSATV. Mice subsequently immunized with 50 nmol of this peptide developed severe EAE within 3 wk, and their T cell-enriched inguinal lymph node cells responded specifically to this peptide. Control mice immunized to proteolipid peptide 202-217 DARMYGVLPWNAFPGK did not develop experimental allergic encephalomyelitis, and their inguinal lymph node cells were unresponsive to either peptide. Thus, a peptide corresponding to a sequence within the proteolipid protein can produce classical acute experimental allergic encephalomyelitis. This is the first report of a synthetic encephalitogenic peptide from myelin proteolipid protein.
The prognostic significance of fluorodeoxyglucose positron emission tomography imaging for patients with nonsmall cell lung carcinoma (1998)

On PET studies of patients with lung carcinoma, FDG uptake within the primary lesion correlates with survival.
Private Knowledge Transfer via Model Distillation with Generative Adversarial Networks (2020)

The deployment of deep learning applications has to address the growing privacy concerns when using private and sensitive data for training. A conventional deep learning model is prone to privacy attacks that can recover the sensitive information of individuals from either model parameters or accesses to the target model. Recently, differential privacy that offers provable privacy guarantees has been proposed to train neural networks in a privacy-preserving manner to protect training data. However, many approaches tend to provide the worst case privacy guarantees for model publishing, inevitably impairing the accuracy of the trained models. In this paper, we present a novel private knowledge transfer strategy, where the private teacher trained on sensitive data is not publicly accessible but teaches a student to be publicly released. In particular, a three-player (teacher-student-discriminator) learning framework is proposed to achieve trade-off between utility and privacy, where the student acquires the distilled knowledge from the teacher and is trained with the discriminator to generate similar outputs as the teacher. We then integrate a differential privacy protection mechanism into the learning procedure, which enables a rigorous privacy budget for the training. The framework eventually allows student to be trained with only unlabelled public data and very few epochs, and hence prevents the exposure of sensitive training data, while ensuring model utility with a modest privacy budget. The experiments on MNIST, SVHN and CIFAR-10 datasets show that our students obtain the accuracy losses w.r.t teachers of 0.89%, 2.29%, 5.16%, respectively with the privacy bounds of (1.93, 10^-5), (5.02, 10^-6), (8.81, 10^-6). When compared with the existing works \cite{papernot2016semi,wang2019private}, the proposed work can achieve 5-82% accuracy loss improvement.
Role of β-Cells in Type 1 Diabetes Pathogenesis (2005)

Whether autoimmunity results primarily from a defect of the immune system, target organ dysfunction, or both remains an open issue in most human autoimmune diseases. The highly multigenic background on which diabetes develops in the NOD mouse and in the human suggests that numerous gene variants associate in contributing to activation of autoimmunity to beta-cells. Both immune genes and islet-related genes are involved. The presence of beta-cells is required for initiation of diabetes autoimmunity to proceed. Available experiments in the NOD mouse and epidemiological evidence in the human point to proinsulin as a key autoantigen in diabetes. The functional importance of insulin, the high number of autoantigens characterized at different stages of diabetes, and their clustering within beta-cell subparticles point to the islet as a starting point in the initiation phase of the disease. Genes that direct the autoimmune reaction toward the beta-cell target, autoantigens that are recognized by autoreactive B- and T-cells along the autoimmune process, the importance of beta-cells in the activation of autoreactive lymphocytes, and the expression level of key beta-cell molecules along diabetes development are successively considered in this review.