gebhart/patrepeval huggingface dataset:
Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands (2013)

Cytosine, 5-methylcytosine, and 5-hydroxymethylcytosine were identified during translocation of single DNA template strands through a modified Mycobacterium smegmatis porin A (M2MspA) nanopore under control of phi29 DNA polymerase. This identification was based on three consecutive ionic current states that correspond to passage of modified or unmodified CG dinucleotides and their immediate neighbors through the nanopore limiting aperture. To establish quality scores for these calls, we examined ~3,300 translocation events for 48 distinct DNA constructs. Each experiment analyzed a mixture of cytosine-, 5-methylcytosine-, and 5-hydroxymethylcytosine-bearing DNA strands that contained a marker that independently established the correct cytosine methylation status at the target CG of each molecule tested. To calculate error rates for these calls, we established decision boundaries using a variety of machine-learning methods. These error rates depended upon the identity of the bases immediately 5' and 3' of the targeted CG dinucleotide, and ranged from 1.7% to 12.2% for a single-pass read. We estimate that Q40 values (0.01% error rates) for methylation status calls could be achieved by reading single molecules 5-19 times depending upon sequence context.
Kinetics, Stoichiometry, and Identification of the Reactive Thiolate in the Inactivation of UDP-GlcNAc Enolpyruvoyl Transferase by the Antibiotic Fosfomycin (1994)

Fosfomycin [(1R,2S)-1,2-epoxypropylphosphonic acid] has been shown to exert its antibiotic effect through the inhibition of UDP-GlcNAc enolpyruvoyl transferase [Kahan, F. M., et al. (1974) Ann. N.Y. Acad. Sci. 235, 364], the enzyme responsible for catalyzing the first committed step in bacterial cell wall biosynthesis. Time-dependent inactivation of MurZ by fosfomycin was found to be greatly accelerated by the presence of cosubstrate UDP-GlcNAc but could also be speeded appreciably by the unreactive substrate analog 3-deoxy-UDP-GlcNAc. These results argue against a reaction-based participation of the cosubstrate and suggest that UDP-GlcNAc has a role in influencing active site conformation critical to the inactivation event. A study of the influence of UDP-GlcNAc and fosfomycin on the kinetics of inactivation allowed the determination of dissociation constants for fosfomycin (KF = 8.6 microM) and UDP-GlcNAc (KS = 14 microM), in addition to a limiting inactivation rate constant (k(inact) = 7.4 min-1) at saturating UDP-GlcNAc and fosfomycin concentrations. Mass spectrometry of inactivated MurZ demonstrated an increase in molecular weight of 138, consistent with the covalent addition of a molar equivalent of fosfomycin (136 kDa). Titration of MurZ with fosfomycin revealed a stoichiometry of 1 molecule of inhibitor per active site when assessed using either enzyme activity or mass spectrometry as an index of modification. Peptide mapping of tryptic digests of fosfomycin-inactivated MurZ revealed modification of a unique 41-mer, the sequence of which revealed that Cys115 was the site of attachment of fosfomycin.
Decreased production of mast cells in S1/S1d anemic mice (1979)

Abstract Production of tissue mast cells was evaluated in genetically anemic mice of S1/S1dgenotype. In the skin of adult S1/S1d mice the numbers of mast cells per centimeter were less than 1 % of the numbers observed in congenic + /+ mice, as reported for adult W/Wv mice. Any mast cells were scarcely detected in other tissues in both S1/S1d and W/Wv mice. Since bone marrow cell transplantation from S1/S1d mice increases the numbers of mast cells in the skin, stomach, and mesentery of W/Wv mice, the bone marrow of S1/S1d mice would seem to contain precursors of mast cells. These precursor cells may arrive at peripheral tissues, as is suggested by the observation that the numbers of mast cells increase in the skin of W/Wv mice grafted to S1/S1drecipients. The lack of mast cells in the S1/S1d mice seems to be due to a tissue defect that locally induces the differentiation of mast cells, as is indicated by the observation that bone marrow transplantation from + /+ donors does not increase the numbers of mast cells in the skin, stomach, and mesentery of S1/S1d mice and the observation that mast cells do not develop in skin of S1/S1d mice grafted to + /+ recipients.
Real-Time Polymerase Chain Reaction MicroRNA Detection Based on Enzymatic Stem-Loop Probes Ligation (2009)

MiRNAs (microRNAs) are a group of endogenous, small noncoding RNA with the length of 18-25 nucleotides, which have recently been demonstrated to play important roles in a wide range of biological processes. In this work, we developed a simple, sensitive, specific, and inexpensive assay through the combination of enzymatic probe ligation and real-time PCR amplification for the measurement of mature miRNAs. A couple of novel DNA probes with a stem-loop structure were implemented to reduce nonspecific ligation by at least 100-fold. The assay has several remarkable features including wide dynamic range, low total RNA input (0.02-0.2 ng), distinct anti-interference from precursor miRNAs (signal-to-noise ratio > 500), and single-base mismatch discrimination among miRNA sequences. In addition, a one-tube assay could be accomplished by designing a couple of universal probes, which makes it feasible to examine the expression of a whole family of miRNA (such as let-7) at one time. Finally, we validated the method for quantifying the expression of four mature miRNAs including miR-122, miR-1, miR-34a, and let-7a across 10 mouse tissues, where U6 snRNA could be simultaneously examined as an endogenous control. Thus, this method revealed a great potential for miRNA quantitation in ordinary laboratory studies and clinical diagnoses.
Photophysical effects of metal-carbon .sigma. bonds in ortho-metalated complexes of iridium(III) and rhodium(III) (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotophysical effects of metal-carbon .sigma. bonds in ortho-metalated complexes of iridium(III) and rhodium(III)S. Sprouse, K. A. King, P. J. Spellane, and Richard J. WattsCite this: J. Am. Chem. Soc. 1984, 106, 22, 6647–6653Publication Date (Print):October 1, 1984Publication History Published online1 May 2002Published inissue 1 October 1984https://pubs.acs.org/doi/10.1021/ja00334a031https://doi.org/10.1021/ja00334a031research-articleACS PublicationsRequest reuse permissionsArticle Views8169Altmetric-Citations726LEARN 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
Real-time two-photon fluorescence microscopy of blood flow dynamics following photothrombotic stroke in rat neocortex (2004)

We use two-photon microscopy to observe changes in blood flow after localized photothrombotic clotting of individual blood vessels in rat neocortex. We find that flow reverses direction downstream from clotted arterioles, thereby maintaining tissue perfusion.
Clonogenic hepatoblasts, common precursors for hepatocytic and biliary lineages, are lacking classical major histocompatibility complex class I antigen (2000)

An in vitro colony-forming assay and flow cytometry were used to identify rat hepatoblasts as being classical MHC class I, RT1A(l-), OX18(low) intercellular adhesion molecule 1 (ICAM-1)(+). Inducible differentiation toward biliary lineage was observed in most colonies derived from single RT1A(l-) progenitors, proving their bipotentiality. These findings demonstrate the antigenic profile of clonogenic hepatoblasts and proof of their bipotency. Furthermore, whereas colony formation of adult hepatocytes required epidermal growth factor, clonal growth of hepatoblasts was potentiated without epidermal growth factor. The adult hepatic colonies consisted of RT1A(l+)OX18(+)ICAM-1(++) cells. These results indicate that hepatoblasts possess unique characteristics as compared with adult hepatocytes harboring significant proliferative activity. The phenotypic identity of hepatoblasts and the clonal culture system have relevance for identifying hepatic stem cells from adults, for studying liver development, and for cell therapy based on hepatic progenitors.
Identification of universal mRNA markers for noninvasive prenatal screening of trisomies (2010)

Plasma was the most suitable tool to be employed in the detection and dosage of placental transcripts. betahCG transcript together with maternal age could be a potential marker for noninvasive prenatal screening of fetal trisomy 21.
Development of Novel Adenoviral Vectors to Overcome Challenges Observed With HAdV-5–based Constructs (2015)

Recombinant vectors based on human adenovirus serotype 5 (HAdV-5) have been extensively studied in preclinical models and clinical trials over the past two decades. However, the thorough understanding of the HAdV-5 interaction with human subjects has uncovered major concerns about its product applicability. High vector-associated toxicity and widespread preexisting immunity have been shown to significantly impede the effectiveness of HAdV-5-mediated gene transfer. It is therefore that the in-depth knowledge attained working on HAdV-5 is currently being used to develop alternative vectors. Here, we provide a comprehensive overview of data obtained in recent years disqualifying the HAdV-5 vector for systemic gene delivery as well as novel strategies being pursued to overcome the limitations observed with particular emphasis on the ongoing vectorization efforts to obtain vectors based on alternative serotypes.
Principles of electrokinetic remediation (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPrinciples of electrokinetic remediationYalcin B. Acar and Akram N. AlshawabkehCite this: Environ. Sci. Technol. 1993, 27, 13, 2638–2647Publication Date (Print):December 1, 1993Publication History Published online1 May 2002Published inissue 1 December 1993https://pubs.acs.org/doi/10.1021/es00049a002https://doi.org/10.1021/es00049a002research-articleACS PublicationsRequest reuse permissionsArticle Views5713Altmetric-Citations1126LEARN 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
Association Between Venous Thromboembolism and Perioperative Allogeneic Transfusion (2007)

In this large observational study of patients undergoing colorectal cancer resection, perioperative allogeneic blood transfusion was associated with an increased risk of VTE in women but not in men. Given the substantial morbidity and mortality associated with VTE and the implication that this finding has for postoperative management in women, this association must be confirmed in independent studies.
Asymmetric bioreduction of activated alkenes to industrially relevant optically active compounds (2012)

Ene-reductases from the 'Old Yellow Enzyme' family of flavoproteins catalyze the asymmetric reduction of various α,β-unsaturated compounds at the expense of a nicotinamide cofactor. They have been applied to the synthesis of valuable enantiopure products, including chiral building blocks with broad industrial applications, terpenoids, amino acid derivatives and fragrances. The combination of these highly stereoselective biocatalysts with a cofactor recycling system has allowed the development of cost-effective methods for the generation of optically active molecules, which is strengthened by the availability of stereo-complementary enzyme homologues.
An introduction to hidden Markov models (1986)

The basic theory of Markov chains has been known to mathematicians and engineers for close to 80 years, but it is only in the past decade that it has been applied explicitly to problems in speech processing. One of the major reasons why speech models, based on Markov chains, have not been developed until recently was the lack of a method for optimizing the parameters of the Markov model to match observed signal patterns. Such a method was proposed in the late 1960's and was immediately applied to speech processing in several research institutions. Continued refinements in the theory and implementation of Markov modelling techniques have greatly enhanced the method, leading to a wide range of applications of these models. It is the purpose of this tutorial paper to give an introduction to the theory of Markov models, and to illustrate how they have been applied to problems in speech recognition.
D2 Dopamine Receptor A1 Allele in Alzheimer Disease and Aging (1997)

The A1 allele does not contribute to AD risk, alone or in combination with the APOE*4 allele. The DRD2 A1 allele frequencies decrease with age in both patients and controls. Thus, studies of DRD2 disease association need to control for age.
Low density lipoprotein undergoes oxidative modification in vivo. (1989)

It has been proposed that low density lipoprotein (LDL) must undergo oxidative modification before it can give rise to foam cells, the key component of the fatty streak lesion of atherosclerosis. Oxidation of LDL probably generates a broad spectrum of conjugates between fragments of oxidized fatty acids and apolipoprotein B. We now present three mutually supportive lines of evidence for oxidation of LDL in vivo: (i) Antibodies against oxidized LDL, malondialdehyde-lysine, or 4-hydroxynonenal-lysine recognize materials in the atherosclerotic lesions of LDL receptor-deficient rabbits; (ii) LDL gently extracted from lesions of these rabbits is recognized by an antiserum against malondialdehyde-conjugated LDL; (iii) autoantibodies against malondialdehyde-LDL (titers from 512 to greater than 4096) can be demonstrated in rabbit and human sera.
Intracellulartransduction using cell-penetrating peptides (2009)

Cell penetrating peptides (CPPs), TATp, in particular, has been used widely for intracellular delivery of various agents ranging from small molecules to proteins, peptides, range of pharmaceutical nanocarriers and imaging agents. This review highlights the mechanisms of CPP-mediated delivery and summarizes numerous examples illustrating the potential of CPPs in the fields of biology and medicine.
Controlled release of drugs: Polymers and aggregate systems (1989)

The incorporation of active materials in a package or matrix to effect controlled or sustained release of drugs to a targeted area is of high research interest. The nine review articles by leading researchers in this book examine from a multidisciplinary perspective the newest systems and phenomena in this fast-moving field. Topics considered are span polymers (bioactive polymers, biodegradable polymers), microcapsules, biomolecules (liposomes), skin (trans-dermal delivery) and novel drug delivery systems (osmotic pumps). Throughout these discussions the focus is placed on the controlled release of active substances in both time and space (delivery rate and site) to obtain a therapeutic or desired effect.
Functional genomics of motile commensal intestinal bacteria (2013)

Flagella confer upon bacteria the ability to move and are therefore organelles of significant bacteriological importance. The innate immune system has evolved to recognise flagellin, (the major protein component of the bacterial flagellar filament). Flagellate microbes can potentially stimulate the immune systems of mammals, and thus have significant immunomodulatory potential. The flagellum-biogenesis genotype and phenotype of Lactobacillus ruminis, an autochthonous intestinal commensal, was studied. The flagellum-biogenesis genotypes of motile enteric Eubacterium and Roseburia species were also investigated. Flagellin proteins were recovered from these commensal species, their amino-termini were sequenced and the proteins were found to be pro-inflammatory, as assessed by measurement of interleukin-8 (IL-8) secretion from human intestinal epithelial cell lines. For L. ruminis, this IL-8 secretion required signalling through Toll Like Receptor 5. A model for the regulation of flagellum-biogenesis in L. ruminis was inferred from transcriptomics data and bioinformatics analyses. Motility gene expression in this species may be under the control of a novel regulator, LRC_15730. Potential promoters for genes encoding flagellin proteins in the Eubacterium and Roseburia genomes analysed were inferred in silico. Relative abundances of the target Eubacterium and Roseburia species in the intestinal microbiota of 25 elderly individuals were determined. These species were found to be variably abundant in these individuals. Motility genes from these species were variably detected in the shotgun metagenome databases generated by the ELDERMET project. This suggested that a greater depth of sequencing, or improved evenness of sequencing, would be required to capture the full diversity of microbial functions for specific target or low abundance species in microbial communities by metagenomics. In summary, this thesis used a functional genomics approach to describe flagellum-mediated motility in selected Gram-positive commensal bacteria. The regulation of flagellum biosynthesis in these species, and the consequences of flagella expression from a host-interaction perspective were also considered.
Multimedia over the Internet (2002)

The paper discusses the motivation, requirements, and the emerging technologies to carry multimedia services over the Internet.
Dry Eye Disease (2012)

Dry eye disease is a multifactorial disorder of the tears and ocular surface characterized by symptoms of dryness and irritation. Although the pathogenesis of dry eye disease is not fully understood, it is recognized that inflammation has a prominent role in the development and propagation of this debilitating condition. Factors that adversely affect tear film stability and osmolarity can induce ocular surface damage and initiate an inflammatory cascade that generates innate and adaptive immune responses. These immunoinflammatory responses lead to further ocular surface damage and the development of a self-perpetuating inflammatory cycle. Herein, we review the fundamental links between inflammation and dry eye disease and discuss the clinical implications of inflammation in disease management.
Mutagenesis of the yellow fever virus NS2B protein: effects on proteolytic processing, NS2B-NS3 complex formation, and viral replication (1993)

To study the role of specific regions of the yellow fever virus NS2B protein in proteolytic processing and association with the NS3 proteinase domain, a series of mutations were created in the hydrophobic regions and in a central conserved hydrophilic region proposed as a domain important for NS2B function. The effects of these mutations on cis cleavage at the 2B/3 cleavage site and on processing at other consensus cleavage sites for the NS3 proteinase in the nonstructural region were then characterized by cell-free translation and transient expression in BHK cells. Association between NS2B and the NS3 proteinase domain and the effects of mutations on complex formation were investigated by nondenaturing immunoprecipitation of these proteins expressed in infected cells, by cell-free translation, or by recombinant vaccinia viruses. Mutations within the hydrophobic regions had subtle effects on proteolytic processing, whereas mutations within the conserved domain dramatically reduced cleavage efficiency or abolished all cleavages. The conserved domain of NS2B is also implicated in formation of an NS2B-NS3 complex on the basis of the ability of mutations in this region to eliminate both association of these two proteins and trans-cleavage activity. In addition, mutations which either eliminated proteolytic processing or had no apparent effect on processing were found to abolish recovery of infectious virus following RNA transfection. These results suggest that the conserved region of NS2B is a domain essential for the function of the NS3 proteinase. Hydrophobic regions of NS2B whose structural integrity may not be essential for proteolytic processing may have additional functions during viral replication.
Testing significance relative to a fold-change threshold is a TREAT (2009)

R code implementing our methods is contributed to the software package limma available at http://www.bioconductor.org.
Purification and Characterization of Single-Wall Carbon Nanotubes (2001)

A purification method has been developed that provides for the removal of metal catalysts and impurity carbon from laser-oven-grown single-wall carbon nanotube (SWNT) material. The oxidation rate of SWNTs in air at elevated temperatures is correlated to the metal content of the sample. Sample purity is documented with SEM, TEM, electron microprobe analysis, Raman, and UV−vis−near-IR. We also note that the relative intensity of the electronic transitions in the near-infrared to the continuum absorption at 400 nm in the UV serves as a useful monitor of the perturbation of the sidewall π-electron density of SWNTs due to sidewall substitution and/or oxidation.
Multi-perspective stereoscopy from light fields (2011)

This paper addresses stereoscopic view generation from a light field. We present a framework that allows for the generation of stereoscopic image pairs with per-pixel control over disparity, based on multi-perspective imaging from light fields. The proposed framework is novel and useful for stereoscopic image processing and post-production. The stereoscopic images are computed as piecewise continuous cuts through a light field, minimizing an energy reflecting prescribed parameters such as depth budget, maximum disparity gradient, desired stereoscopic baseline, and so on. As demonstrated in our results, this technique can be used for efficient and flexible stereoscopic post-processing, such as reducing excessive disparity while preserving perceived depth, or retargeting of already captured scenes to various view settings. Moreover, we generalize our method to multiple cuts, which is highly useful for content creation in the context of multi-view autostereoscopic displays. We present several results on computer-generated content as well as live-action content.
Design of near optimum electrical equalizers for optical transmission in the presence of PMD (2002)

An adaptive Viterbi equalizer and a decision feedback equaliser (DFE) for nonlinear intersymbol interference using a state-based probabilistic approach is proposed. The Viterbi equalizer design is suitable for high data rates and outperforms other concepts for high PMD.