gebhart/patrepeval huggingface dataset:
PTMap—A sequence alignment software for unrestricted, accurate, and full-spectrum identification of post-translational modification sites (2009)

We present sequence alignment software, called PTMap, for the accurate identification of full-spectrum protein post-translational modifications (PTMs) and polymorphisms. The software incorporates several features to improve searching speed and accuracy, including peak selection, adjustment of inaccurate mass shifts, and precise localization of PTM sites. PTMap also automates rules, based mainly on unmatched peaks, for manual verification of identified peptides. To evaluate the quality of sequence alignment, we developed a scoring system that takes into account both matched and unmatched peaks in the mass spectrum. Incorporation of these features dramatically increased both accuracy and sensitivity of the peptide- and PTM-identifications. To our knowledge, PTMap is the first algorithm that emphasizes unmatched peaks to eliminate false positives. The superior performance and reliability of PTMap were demonstrated by confident identification of PTMs on 156 peptides from four proteins and validated by MS/MS of the synthetic peptides. Our results demonstrate that PTMap is a powerful algorithm capable of identification of all possible protein PTMs with high confidence.
Disruption of T Cell Tolerance to Self-Immunoglobulin Causes Polyclonal B Cell Stimulation Followed by Inactivation of Responding Autoreactive T Cells (2000)

Scavenger receptor (SR)-specific delivery by maleylation of a ubiquitous self-protein, Ig, to SR-bearing APCs results in self-limiting induction of autoimmune effects in vivo. Immunization with maleyl-Ig breaks T cell tolerance to self-Ig and causes hypergammaglobulinemia, with increases in spleen weight and cellularity. The majority of splenic B cells show an activated phenotype upon maleyl-Ig immunization, leading to large-scale conversion to a CD138+ phenotype and to significant increases in CD138-expressing splenic plasma cells. The polyclonal B cell activation, hypergammaglobulinemia, and autoreactive Ig-specific T cell responses decline over a 2-mo period postimmunization. Following adoptive transfer, T cells from maleyl-Ig-immune mice taken at 2 wk postimmunization can induce hypergammaglobulinemia in the recipients, but those taken at 10 wk postimmunization cannot. Hypergammaglobulinemia in the adoptive transfer recipients is also transient and is followed by an inability to respond to fresh maleyl-Ig immunization, suggesting that the autoreactive Ig-specific T cells are inactivated peripherally following disruption of tolerance. Thus, although autoreactive T cell responses to a ubiquitous self-Ag, Ig, are induced by SR-mediated delivery to professional APCs in vivo resulting in autoimmune pathophysiological effects, they are effectively and rapidly turned off by inactivation of these activated Ig-specific T cells in vivo.
All classes of murine IgG antibody mediate macrophage phagocytosis and lysis of erythrocytes. (1980)

Antibody-dependent phagocytosis and lysis of sheep RBC by mouse peritoneal exudate cells were studied using IgG subclass fractions of sera prepared by protein A-Sepharose chromatography. Three IgG1, 3 IgG2a, 4 IgG2b, and 1 IgG3 hybridoma antibodies to RBC were also used. The results showed that some monoclonal IgG2a and IgG2b antibodies were more active than IgG1 or IgG3 preparations when normalized to hemagglutinating activity, but all IgG sources mediated both effector mechanisms. This is in accord with findings of strong Fc receptors on macrophages for the IgG2 isotypes and weaker binding by IgG1 and newly discovered IgG3 receptors. A monoclonal IgG2b with no hemagglutination titer showed normal cooperation with macrophages. In contrast, 2 hybridoma IgM were inactive in macrophage-mediated lysis and allowed only marginal ingestion. Similar results were obtained using several macrophage cell lines, mouse spleen and human peripheral blood mononuclear cells, showing that all these types of effector cells do not distinguish among (mouse) IgG subclasses in handling antibody-coated RBC.
The H3K4 methyltransferase Setd1a is first required at the epiblast stage, whereas Setd1b becomes essential after gastrulation (2014)

Histone 3 lysine 4 (H3K4) methylation is a universal epigenetic mark. In mammals, there are six H3K4 methyltransferases related to yeast Set1 and fly Trithorax, including two orthologs of Set1: Setd1a and Setd1b. Here we show that mouse Setd1a is required for gastrulation, whereas Setd1b-deficient embryos survive to E11.5 but are grossly retarded. Setd1a knockout embryos implant but do not proceed past the epiblast. Furthermore, Setd1a is not required until the inner cell mass has formed, at which stage it has replaced Mll2 as the major H3K4 methyltransferase. Setd1a is required for embryonic, epiblast and neural stem cell survival and neural stem cell reprogramming, whereas Setd1b is dispensable. Deletion of Setd1a in embryonic stem cells resulted in rapid losses of bulk H3K4 methylation, pluripotency gene expression and proliferation, with G1 pileup. Setd1b overexpression could not rescue the proliferation defects caused by loss of Setd1a in embryonic stem cells. The precise developmental requirement for Setd1a suggests that gastrulation is regulated by a switch between the major H3K4 methyltransferases.
Trehalose Click Polymers Inhibit Nanoparticle Aggregation and Promote pDNA Delivery in Serum (2006)

Herein, three new glycopolymers have been synthesized via "click polymerization" to promote nucleic acid delivery in the presence of biological media containing serum. These structures were designed to contain a trehalose moiety to promote biocompatibility, water solubility, and stability against aggregation, amide-triazole groups to enhance DNA binding affinity, and an oligoamine unit to facilitate DNA encapsulation, phosphate neutralization, and interactions with cell surfaces. A 2,3,4,2',3',4'-hexa-O-acetyl-6,6'-diazido-6,6'-dideoxy-D-trehalose (4) monomer was polymerized via copper(I)-catalyzed azide-alkyne cycloaddition with a series of dialkyne-amide comonomers that contain either one, two, or three Boc-protected secondary amines (7a, 7b, or 7c, respectively). After deprotection, three water-soluble polycations (9a, 9b, or 9c) were obtained with similar degrees of polymerization (n = 56-61) to elucidate the role of amine number on nucleic acid binding, complex formation, stability, and cellular delivery. Gel electrophoresis and ethidium bromide experiments showed that 9a-9c associated with plasmid DNA (pDNA) and formed complexes (polyplexes) at N/P ratios dependent on the amine number. TEM experiments revealed that 9a-9c polyplexes were small (50-120 nm) and had morphologies (spherical and rodlike) associated with the polymer chain stiffness. Dynamic light scattering studies in the presence of media containing serum demonstrated that 9c polyplexes had a low degree of flocculation, whereas 9a and 9b polyplexesd aggregate rapidly. Further biological studies revealed that these structures were biocompatible and deliver pDNA into HeLa cells. Particularly, 9c polyplexes promoted high delivery efficacy and gene expression profiles in the presence of serum.
Mechanisms of the inhibition of reverse transcription by unmodified and modified antisense oligonucleotides (1993)

We demonstrated that unmodified and modified (phosphorothioate) oligonucleotides prevent cDNA synthesis by AMV or HIV reverse transcriptases. Antisense oligonucleotide/RNA hybrids specifically arrest primer extension. The blockage involves the degradation of the RNA fragment bound to the antisense oligonucleotide by the reverse transcriptase-associated RNase H activity. However, the phosphorothioate oligomer inhibited polymerization by binding to the AMV RT rather than to the template RNA, whereas there was no competitive binding of the phosphorothioate oligomer on the HIV RT during reverse transcription.
A New Anterior Cervical Instrumentation System Combining an Intradiscal Cage With an Integrated Plate (2001)

The design of the system appears to prevent bone-graft recipient site and donor site complications, provides immediate biomechanical stability, prevents screw backout or breakage, and restores posterior interbody height and lordosis. The device is of sufficient promise to warrant further close evaluation focusing on long-term outcome. The new radiolucent version has potential advantages for the assessment of fusion.
Characterization of the Surface Enhanced Raman Scattering (SERS) of Bacteria (2004)

The surface enhanced Raman scattering (SERS) of a number of species and strains of bacteria obtained on novel gold nanoparticle (approximately 80 nm) covered SiO(2) substrates excited at 785 nm is reported. Raman cross-section enhancements of >10(4) per bacterium are found for both Gram-positive and Gram-negative bacteria on these SERS active substrates. The SERS spectra of bacteria are spectrally less congested and exhibit greater species differentiation than their corresponding non-SERS (bulk) Raman spectra at this excitation wavelength. Fluorescence observed in the bulk Raman emission of Bacillus species is not apparent in the corresponding SERS spectra. Despite the field enhancement effects arising from the nanostructured metal surface, this fluorescence component appears "quenched" due to an energy transfer process which does not diminish the Raman emission. The surface enhancement effect allows the observation of Raman spectra of single bacterial cells excited at low incident powers and short data acquisition times. SERS spectra of B. anthracis Sterne illustrate this single cell level capability. Comparison with previous SERS studies reveals how the SERS vibrational signatures are strongly dependent on the morphology and nature of the SERS active substrates. The potential of SERS for detection and identification of bacterial pathogens with species and strain specificity on these gold particle covered glassy substrates is demonstrated by these results.
The Lanthanide Cations as Probes in Biological Systems. Proton Relaxation Enhancement Studies for Model Systems and Lysozyme (1971)

A study has been made over a range of temperatures at 20 MHz and 35 MHz of the spin relaxation rates of water protons in aqueous solutions of ethylene glycol bis-(aminoethyl)-tetraacetic acid containing Gd(III) and Eu(II) ions. The results suggest that the dominant relaxation process arises from rotation of the solvated complexes. Relaxation enhancement has been observed for Gd(III) in the presence of lysozyme and values of ɛ*, Kd and τc have been determined. An application of these results to obtain distances of substrate analogues from the active site of this and other enzymes is discussed.
Durable Complete Response of Metastatic Gastric Cancer with Anti-Met Therapy Followed by Resistance at Recurrence (2011)

This research brief is the first to describe a durable complete response obtained with a molecularly targeted monoclonal antibody, MetMAb, to the receptor tyrosine kinase, Met, in a patient with chemorefractory metastatic gastric cancer. It is also the first to report biomarkers that predicted therapeutic response to Met inhibition.
Specificity and Topology of the Escherichia coli Xanthosine Permease, a Representative of the NHS Subfamily of the Major Facilitator Superfamily (2001)

The specificity of XapB permease was compared with that of the known nucleoside transporters NupG and NupC. XapB-mediated xanthosine uptake is abolished by 2,4-dinitrophenol and exhibits saturation kinetics with an apparent K(m) of 136 microM. A 12-transmembrane-segment model was confirmed by translational fusions to alkaline phosphatase and the alpha fragment of beta-galactosidase.
Arabidopsis Transcription Factors and the Regulation of Flowering Time: A Genomic Perspective (2002)

The availability of the Arabidopsis genome sequence allows for novel approaches in the analysis of many aspects of plant biology. Approximately 6% of Arabidopsis genes code for transcription factors, which can be grouped into different families according to similarities within the DNA binding domains. Transcription factors are critical regulatory components of the pathways that underpin many aspects of plant growth, development, and physiology. In particular, a substantial number of them are emerging as having crucial roles in controlling one of the most important, but complex, steps in the plant life cycle: the transition to flowering. Genome-wide studies offer the opportunity to gain a comprehensive understanding of this polygenic process, making it possible to appreciate both the large number of genes involved, as well as the complex regulatory networks into which those genes are integrated.
Assessment and Classroom Learning (1998)

ABSTRACT This article is a review of the literature on classroom formative assessment. Several studies show firm evidence that innovations designed to strengthen the frequent feedback that students receive about their learning yield substantial learning gains. The perceptions of students and their role in self‐assessment are considered alongside analysis of the strategies used by teachers and the formative strategies incorporated in such systemic approaches as mastery learning. There follows a more detailed and theoretical analysis of the nature of feedback, which provides a basis for a discussion of the development of theoretical models for formative assessment and of the prospects for the improvement of practice.
Alkylations at the Methyl or α-Methylene Group of 6- or 4-Alkyl-3-cyano-2(1)-pyridones through Dianions1 (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlkylations at the Methyl or α-Methylene Group of 6- or 4-Alkyl-3-cyano-2(1)-pyridones through Dianions1Sandra Boatman, Thomas M. Harris, and Charles R. HauserCite this: J. Org. Chem. 1965, 30, 11, 3593–3597Publication Date (Print):November 1, 1965Publication History Published online1 May 2002Published inissue 1 November 1965https://pubs.acs.org/doi/10.1021/jo01022a003https://doi.org/10.1021/jo01022a003research-articleACS PublicationsRequest reuse permissionsArticle Views116Altmetric-Citations8LEARN 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
Transfection by DNA-nuclear protein HMG1 complexes: raising of efficiency and role of DNA topology. (1990)

We have developed a novel and efficient transfection method based on the introduction of foreign DNA into mammalian cells in form of complexes of vector DNA with the nuclear protein HMG1. In this study, it is shown that a stabilization of the complexes against dilution dissociation by addition of soluble CaCl2 or by excessive HMG1 enhances the transfection efficiency. Furthermore, there are no differences in the transfection abilities between the 3 topological DNA forms, viz., supercoiled, open relaxed and linear DNA, if delivered to cells as HMG1-DNA complexes. It is further shown that transfection-inactive complexes of the core histones with foreign DNA can be activated in transfection by the addition of HMG1.
Effect of Emblica officinalis tannoids on a rat model of tardive dyskinesia. (2000)

Effect of active tannoid principles of E. officinalis, comprising of emblicanin A (37%), emblicanin B (33%), punigluconin (12%) and pedunculagin (14%), was investigated on a rat model of tardive dyskinesia (TD) induced by once daily administration of haloperidol (1.5 mg/kg, ip) for 28 days. Involuntary orofacial movements (chewing movements, buccal tremors and tongue protusion) were assessed as TD parameters. The tannoid principles of E. officinalis (EOT) were administered concomitantly with haloperidol in the doses of 10, 20 and 50 mg/kg, po, for 28 days. Sodium valproate (200 mg/kg, po), a Gaba-mimetic agent, and vitamin E (400 mg/kg, po), an antioxidant, were used as the standard drugs and administered for the same period. EOT induced a dose-related inhibition of all the three TD parameters assessed, as did vitamin E. The effect of sodium valproate remained statistically insignificant. The results suggest that EOT exerts a prophylactive effect against neuroleptic-induced TD which is likely to be due to its earlier reported antioxidant effects in rat brain areas, including striatum.
International children's continence society's recommendations for therapeutic intervention in congenital neuropathic bladder and bowel dysfunction in children (2012)

Guidelines on pharmalogical and surgical intervention are presented. First the multiple modalities for intervention that do not involve surgical reconstruction are summarized concerning pharmacological agents, medical devices, and neuromodulation. The non-surgical intervention is promoted before undertaking major surgery. Indicators for non-surgical treatments depend on issues related to intravesical pressure, upper urinary tract status, prevalence of urinary tract infections, and the degree of incontinence. The optimal age for treatment of incontinence is also addressed. This is followed by a survey of specific treatments such as anticholinergics, botulinum-A toxin, antibiotics, and catheters. Neuromodulation of the bladder via intravesical electrical stimulation, sacral nerve stimulation, transcutaneous stimulation, and biofeedback is scrutinized. Then follows surgical intervention, which should be tailored to each individual, based on careful consideration of urodynamic findings, medical history, age, and presence of other disability. Treatments mentioned are: urethral dilation, vesicostomy, bladder, augmentation, fascial sling, artificial urinary sphincters, and bladder neck reconstruction and are summarized with regards to success rates and complications. Finally, the treatment on neuropathic bowel dysfunction with rectal suppositories irrigation and transrectal stimulation are scrutinized.
Three-dimensional analysis by a microlens-array confocal arrangement (1994)

Scanning confocal microscopy is now well developed and applied. As an alternative to a laser spot to be scanned, parallel processing can be obtained when a two-dimensional structure is moved through the focal plane and a series of image sections is recorded. Surface topography is determined by analysis of the normalized intensity of the appropriate image points, i.e., a search of the intensity maximum leads to surface coordinates. With a high numerical aperture of the optical system, the half-width of I(z) is small, and the topography can be calculated with high accuracy. But with a high numerical aperture, only small object fields can be reproduced. As an alternative to the Nipkow disk for parallel processing, high-numerical-aperture microlenses are combined in an array. The reproducible object field is then limited by the size of the array and the number of lens and detector elements.
Cell-associated West Nile flavivirus is covered with E+pre-M protein heterodimers which are destroyed and reorganized by proteolytic cleavage during virus release (1989)

Flaviviruses are enveloped viruses which accumulate in cellular vacuoles prior to release. The membrane of cell-associated virus contains the proteins pre-M and E. During release of virus the pre-M protein is cleaved, and only its carboxy-terminal segment remains associated with the virus as M protein. Studies of the association of membrane proteins of intracellular and extracellular particles of West Nile virus show that in cell-associated virus the pre-M and E proteins are present as E+pre-M heterodimers. Cleavage of pre-M during release leads to dissociation of the heterodimers: the amino-terminal region of the pre-M protein is lost from the virus, whereas the proteins M and E remain associated with the viral membrane as separate molecules. The E protein of extracellular virus has a tendency to oligomerize into trimers, and both E-protein monomers and trimers are present on extracellular virions. We have prepared partially purified extracellular virus without loss of viral infectivity. These preparations contain approximately 600 physical particles for each PFU. Since purification of cell-associated virus results in significant loss of PFU, an inactivation of virus may occur during this procedure. Preparations of cell-associated virus contained approximately 40,000 physical particles for each PFU.
A Taxi Order Dispatch Model based On Combinatorial Optimization (2017)

Taxi-booking apps have been very popular all over the world as they provide convenience such as fast response time to the users. The key component of a taxi-booking app is the dispatch system which aims to provide optimal matches between drivers and riders. Traditional dispatch systems sequentially dispatch taxis to riders and aim to maximize the driver acceptance rate for each individual order. However, the traditional systems may lead to a low global success rate, which degrades the rider experience when using the app. In this paper, we propose a novel system that attempts to optimally dispatch taxis to serve multiple bookings. The proposed system aims to maximize the global success rate, thus it optimizes the overall travel efficiency, leading to enhanced user experience. To further enhance users' experience, we also propose a method to predict destinations of a user once the taxi-booking APP is started. The proposed method employs the Bayesian framework to model the distribution of a user's destination based on his/her travel histories.
Probability densities of second-order polarization mode dispersion including polarization dependent chromatic fiber dispersion (2000)

We describe experiments and simulation of second-order polarization mode dispersion (PMD) components in optical fibers with emphasis on polarization-dependent chromatic dispersion (PCD). Excellent agreement is found in comparisons of experimental, simulated, and theoretical probability densities. To our knowledge, these are the first such comparisons for the second-order PMD magnitude and the PCD.
Femtosecond-Time-Resolved Surface Structural Dynamics of Optically Excited Silicon (1983)

The dynamics of the structural changes that take place on a silicon surface following excitation with an intense optical pulse are observed with 90-fs time resolution. The threefold rotational symmetry of the silicon $〈111〉$ surface becomes rotationally isotropic within a picosecond after excitation consistent with a transition from the crystalline to the liquid molten state.