gebhart/patrepeval huggingface dataset:
A Novel method for the simultaneous identification of methylcytosine and hydroxymethylcytosine at a single base resolution (2016)

Since the discovery of oxidative demethylation of methylcytosine (mC) by Tet enzymes, an analytical method has been urgently needed that would enable the identification of mC and hydroxymethylcytosine (hmC) at the single base resolution level, because their roles in gene regulation are quite different from each other. However, the bisulfite sequencing method, the gold standard for DNA methylation analysis at present, does not distinguish them. Recently reported alternative methods, such as oxBS-seq and TAB-seq, are not even capable of determining mC and hmC simultaneously. Here, we report a novel method for the direct identification of mC, hmC and unmodified cytosine (C) at a single base resolution. We named this method the Enzyme-assisted Identification of Genome Modification Assay (EnIGMA), and it was demonstrated to indeed have a highly efficient and reliable analytic capacity for distinguishing them. We also successfully applied this novel method to the analysis of the maintenance of the DNA methylation status of imprinted H19-DMR. Importantly, hydroxymethylation plays an ambivalent role in the maintenance of the genome imprinting memory in parental genomes essential for normal development, shedding new light on the epigenetic regulation in ES cells.
RF Power Amplifier Linearization in Professional Mobile Radio Communications Using Artificial Neural Networks (2018)

This paper is focused on the linearization of the radio frequency power amplifier of a professional digital handheld by means of an artificial neural network. The simplicity of the neural network that is used, together with the fact that a feedback path is unnecessary, makes this solution ideal to reduce both the cost of a handheld and its hardware complexity, while fully maintaining its performance. A compensation system is also needed to keep the linearization characteristics of the neural network stable against frequency, temperature, and voltage variations. The whole solution that comprises both the neural network and the compensation system has been implemented in the digital signal processor of a real handheld and afterward fully tested. It has proved to be satisfactory to meet the telecommunication standard requirements in all frequency, temperature, and voltage ranges under consideration while efficient to lower the computational cost of the handheld and to make its internal hardware simpler in comparison with other traditional linearization techniques. The results obtained demonstrate that a neural network can be used to linearize the power amplifiers that are used in transmitters of telecommunication equipment, leading to a significant reduction of both their hardware cost and complexity.
Alteration of the specificity of the cofactor-binding pocket of Corynebacterium 2,5-diketo-D-gluconic acid reductase A (2002)

The NADPH-dependent 2,5-diketo-D-gluconic acid (2,5-DKG) reductase enzyme is a required component in some novel biosynthetic vitamin C production processes. This enzyme catalyzes the conversion of 2,5-DKG to 2-keto-L-gulonic acid, which is an immediate precursor to L-ascorbic acid. Forty unique site-directed mutations were made at five residues in the cofactor-binding pocket of 2,5-DKG reductase A in an attempt to improve its ability to use NADH as a cofactor. NADH is more stable, less expensive and more prevalent in the cell than is NADPH. To the best of our knowledge, this is the first focused attempt to alter the cofactor specificity of a member of the aldo-keto reductase superfamily by engineering improved activity with NADH into the enzyme. Activity of the mutants with NADH or NADPH was assayed using activity-stained native polyacrylamide gels. Eight of the mutants at three different sites were identified as having improved activity with NADH. These mutants were purified and subjected to a kinetic characterization with NADH as a cofactor. The best mutant obtained, R238H, produced an almost 7-fold improvement in catalysis with NADH compared with the wild-type enzyme. Surprisingly, most of this catalytic improvement appeared to be due to an improvement in the apparent kcat for the reaction rather than a large improvement in the affinity of the enzyme for NADH.
IgM Production by Bone Marrow Plasmablasts Contributes to Long-Term Protection against Intracellular Bacterial Infection (2010)

IgM responses are well known to occur early postinfection and tend to be short-lived, which has suggested that this Ig does not significantly contribute to long-term immunity. In this study, we demonstrate that chronic infection with the intracellular bacterium Ehrlichia muris elicits a protective, long-term IgM response. Moreover, we identified a population of CD138(high)IgM(high) B cells responsible for Ag-specific IgM production in the bone marrow. The IgM-secreting cells, which exhibited characteristics of both plasmablasts and plasma cells, contributed to protection against fatal ehrlichial challenge. Mice deficient in activation-induced cytidine deaminase, which produce only IgM, were protected against fatal ehrlichial challenge infection. The IgM-secreting cells that we have identified were maintained in the bone marrow in the absence of chronic infection, as antibiotic-treated mice remained protected against challenge infection. Our studies identify a cell population that is responsible for the IgM production in the bone marrow, and they highlight a novel role for IgM in the maintenance of long-term immunity during intracellular bacterial infection.
Return to the Past: The Case for Antibody-Based Therapies in Infectious Diseases (1995)

In the preantibiotic era, passive antibody administration (serum therapy) was useful for the treatment of many infectious diseases. The introduction of antimicrobial chemotherapy in the 1940s led to the rapid abandonment of many forms of passive antibody therapy. Chemotherapy was more effective and less toxic than antibody therapy. In this last decade of the 20th century the efficacy of antimicrobial chemotherapy is diminishing because of the rapidly escalating number of immunocompromised individuals, the emergence of new pathogens, the reemergence of old pathogens, and widespread development of resistance to antimicrobial drugs. This diminishment in the effectiveness of chemotherapy has been paralleled by advances in monoclonal antibody technology that have made feasible the generation of human antibodies. This combination of factors makes passive antibody therapy an option worthy of serious consideration. We propose that for every pathogen there exists an antibody that will modify the infection to the benefit of the host. Such antibodies are potential antimicrobial agents. Antibody-based therapies have significant advantages and disadvantages relative to standard chemotherapy. The reintroduction of antibody-based therapy would require major changes in the practices of infectious disease specialists.
Epitope mapping of the variable repetitive region with the MB antigen of Ureaplasma urealyticum (1996)

One of the major surface structures of Ureaplasma urealyticum recognized by antibodies of patients during infection is the MB antigen. Previously, we showed by Western blot (immunoblot) analysis that any one of the anti-MB monoclonal antibodies (MAbs) 3B1.5, 5B1.1, and 10C6.6 could block the binding of patient antibodies to MB. Subsequent DNA sequencing revealed that a unique six-amino-acid direct tandem repeat region composed the carboxy two-thirds of this antigen. In the present study, using antibody-reactive peptide scanning of this repeat region, we demonstrated that the amino acids defining the epitopes for MAbs 3B1.5 5B1.1 and 10C6.6 are EQP, GK, and KEQPA, respectively. Peptide scanning analysis of an infected patient's serum antibody response showed that the dominant epitope was defined by the sequence PAGK. Mapping of these continuous epitopes revealed overlap between all MAb and patient polyclonal antibody binding sites, thus explaining the ability of a single MAb to apparently block all polyclonal antibody binding sites. We also show that a single amino acid difference in the sequence of the repeats of serovars 3 and 14 accounts for the lack of reactivity with serovar 14 of two of the serovar 3-specific MAbs. Finally, the data demonstrate the need to obtain the sequences of the mba genes of all serovars before an effective serovar-specific antibody detection method can be developed.
Enzymes in Nonaqueous Solvents: Applications in Carbohydrate and Peptide Preparation (2003)

In nature, the vast majority of enzyme-catalyzed reactions are carried out in water. Traditionally, enzymic catalysis in organic synthesis is carried out in aqueous
High Throughput Genome-Wide Survey of Small RNAs from the Parasitic Protists Giardia intestinalis and Trichomonas vaginalis (2009)

RNA interference (RNAi) is a set of mechanisms which regulate gene expression in eukaryotes. Key elements of RNAi are small sense and antisense RNAs from 19 to 26 nt generated from double-stranded RNAs. MicroRNAs (miRNAs) are a major type of RNAi-associated small RNAs and are found in most eukaryotes studied to date. To investigate whether small RNAs associated with RNAi appear to be present in all eukaryotic lineages, and therefore present in the ancestral eukaryote, we studied two deep-branching protozoan parasites, Giardia intestinalis and Trichomonas vaginalis. Little is known about endogenous small RNAs involved in RNAi of these organisms. Using Illumina Solexa sequencing and genome-wide analysis of small RNAs from these distantly related deep-branching eukaryotes, we identified 10 strong miRNA candidates from Giardia and 11 from Trichomonas. We also found evidence of Giardia short-interfering RNAs potentially involved in the expression of variant-specific surface proteins. In addition, eight new small nucleolar RNAs from Trichomonas are identified. Our results indicate that miRNAs are likely to be general in ancestral eukaryotes and therefore are likely to be a universal feature of eukaryotes.
Regulatory role of collagen V in establishing mechanical properties of tendons and ligaments is tissue dependent (2015)

Patients with classic (type I) Ehlers-Danlos syndrome (EDS), characterized by heterozygous mutations in the Col5a1 and Col5a2 genes, exhibit connective tissue hyperelasticity and recurrent joint dislocations, indicating a potential regulatory role for collagen V in joint stabilizing soft tissues. This study asked whether the contribution of collagen V to the establishment of mechanical properties is tissue dependent. We mechanically tested four different tissues from wild type and targeted collagen V-null mice: the flexor digitorum longus (FDL) tendon, Achilles tendon (ACH), the anterior cruciate ligament (ACL), and the supraspinatus tendon (SST). Area was significantly reduced in the Col5a1(ΔTen/ΔTen) group in the FDL, ACH, and SST. Maximum load and stiffness were reduced in the Col5a1(ΔTen/ΔTen) group for all tissues. However, insertion site and midsubstance modulus were reduced only for the ACL and SST. This study provides evidence that the regulatory role of collagen V in extracellular matrix assembly is tissue dependent and that joint instability in classic EDS may be caused in part by insufficient mechanical properties of the tendons and ligaments surrounding each joint.
Multi-context photo browsing on mobile devices based on tilt dynamics (2007)

This paper presents a photo browsing system on mobile devices to browse and search photos efficiently by tilting action. It employs tilt dynamics and a multi-scale photo screen layout for enhancing the browsing and the search capability respectively. The implementation uses continuous inputs from an accelerometer, and a multimodal (visual, audio and vibrotactile) display coupled with the states of this model. The model is based on a simple physical model, with its characteristics shaped to enhance controllability. The multi-scale layout holds both local and global view for users to both control photos and look at the surrounding context in a single framework. The experiment on Samsung MITs PDA used seven novice users browsing from 100 photos. We compare a tilt-based interaction method with a button-based browser and an iPod wheel by a quantitative usability criteria and subjective experience. The proposed tilt dynamics improves the usability over conventional dynamics. The iPod wheel has mixed performance comparing worse on some metrics than button pushing or tilt interaction, despite its commercial popularity.
A novel multimode interference optoelectronic AND gate with partial index-modulation regions (2002)

A novel smart optoelectronic AND gate based on multimode interference structure has been proposed for the first time. Different from conventional methods, the multimode interference structure is employed to realize the AND logic function. It takes advantages of the linear operation and the easy-to-implement logic function. In this paper, the detailed investigations such as configuration of the logic gate, design rules of MMI structure and simulation results have been considered. Furthermore, the multi-input AND gate can be realized by cascading architectures.
Infrared Spectroscopic Imaging Advances as an Analytical Technology for Biomedical Sciences (2017)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTInfrared Spectroscopic Imaging Advances as an Analytical Technology for Biomedical SciencesTomasz P. Wrobel†∥ and Rohit Bhargava*†§View Author Information† Beckman Institute for Advanced Science and Technology, Urbana, Illinois 61801, United States§ Departments of Bioengineering, Electrical and Computer Engineering, Mechanical Science and Engineering, Chemical and Biomolecular Engineering, and Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States∥ Institute of Nuclear Physics, Polish Academy of Sciences, Krakow, Poland, PL-31342*E-mail: [email protected]Cite this: Anal. Chem. 2018, 90, 3, 1444–1463Publication Date (Web):December 27, 2017Publication History Published online27 December 2017Published inissue 6 February 2018https://pubs.acs.org/doi/10.1021/acs.analchem.7b05330https://doi.org/10.1021/acs.analchem.7b05330review-articleACS PublicationsCopyright © 2017 American Chemical SocietyRequest reuse permissionsArticle Views2696Altmetric-Citations79LEARN 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 SUBJECTS:Biological imaging,Imaging,Infrared light,Lasers,Optical imaging Get e-Alerts
Purification and Characterization of Colicin V from Escherichia coli Culture Supernatants (1994)

The peptide antibiotic, colicin V (ColV), has been purified and characterized from Escherichia coli culture supernatants by precipitation with trichloroacetic acid (TCA) and high-performance liquid chromatography (HPLC). Polyacrylamide gel electrophoresis (PAGE) and Western analysis identifies ColV as a polypeptide with an apparent molecular mass of 5.8 kDa. The protein identified remains biologically active after purification and SDS-PAGE. A mutant form of ColV, ColV-1, removes the carboxy-terminal 21 amino acids and replaces them with eight heterologous residues. The ColV-1 mutant is also secreted into the extracellular medium, demonstrating that the carboxy-terminal 21 amino acids are not required for secretion by the dedicated ColV export system, CvaAB/TolC. N-Terminal amino acid sequencing shows that the primary translation product of cvaC, the ColV structural gene, is processed to remove the N-terminal 15 amino acids. The cleavage site is preceded by the sequence Ser-Gly-Gly, making it a potential substrate for leader peptidase. The ColV leader sequence has many characteristics in common with the amino-terminal leader sequences of the lactococcins, lactacins, and pediocins from Gram-positive bacteria. Mass spectroscopy of purified ColV shows that it has a mass of 8741.0 amu, consistent with the mass of the unmodified 88 amino acid polypeptide. The purification scheme provides a rapid and simple way to obtain ColV for further biochemical analysis.
Quantifier scoping in the SRI core language engine (1988)

An algorithm for generating the possible quantitier scopings for a sentence, in order of preference, is outlined. The scoping assigned to a quanttrier is determined by its interactions with other quanttriers, toodais, negation, and certain syntacticconstituent boundaries. When a potential scoping is logically equivalent to another, the less preferred one is discarded.
Reconstructing Lives — A Tale of Two Soldiers (2006)

As thousands of brain-injured veterans come home to recover and rebuild their lives, medical experts have expressed concern about the challenges of providing them with continuing medical care and vocational and emotional support. To see how two transitions are going, Dr. Susan Okie recently visited Sergeants Jason Pepper and David Emme.
The Redox State of the [2Fe-2S] Clusters in SoxR Protein Regulates Its Activity as a Transcription Factor (1996)

SoxR protein is a redox-responsive transcription factor that governs a regulon of oxidative stress and antibiotic resistance genes in Escherichia coli. Purified SoxR contains oxidized [2Fe-2S] clusters and stimulates in vitro transcription of its target gene soxS up to 100-fold. SoxR transcriptional activity, but not DNA binding, is completely dependent on the [2Fe-2S] clusters; apo-SoxR prepared in vitro binds the soxS promoter with unchanged affinity but does not have transcription activity. Thus, modulation of the SoxR [2Fe-2S] clusters was proposed to control the protein's function in transcription. Here, we provide evidence that SoxR with reduced [2Fe-2S] clusters is inactive. Redox titration of purified SoxR revealed a midpoint potential of -285 +/- 10 mV (pH 7.6). In vitro transcription assays showed that SoxR was inactivated when the [2Fe-2S] cluster was reduced (-380 mV), and full activity was restored upon reoxidation (+100 mV). The results suggest that one-electron oxidation and reduction of the [2Fe-2S] cluster regulate SoxR transcriptional activity.
Inhibitory effect against Akt of cyclic dipeptides isolated from Bacillus sp. (2008)

Among thirteen strains of the genus Bacillus isolated from Shrimp-jeotkal in our laboratory, a strain BA34 showing good antifungal activity against Phytophthora infestans in a previous experiment was tested for the inhibitory effect against Akt, protein kinase B. Since Akt is known to play an important role in controlling apoptosis, its inhibitors can be used as potential apoptosis-inducing agents in the treatment of cancer. Two active compounds were isolated and their structures were determined. They have similar structures, despite showing different inhibitory effects. In order to elucidate the reasons for these different effects, three-dimensional studies were carried out.
ChemInform Abstract: Directed Evolution of Enzymes (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Electromyogram pattern recognition for control of powered upper-limb prostheses: State of the art and challenges for clinical use (2011)

Using electromyogram (EMG) signals to control upper-limb prostheses is an important clinical option, offering a person with amputation autonomy of control by contracting residual muscles. The dexterity with which one may control a prosthesis has progressed very little, especially when controlling multiple degrees of freedom. Using pattern recognition to discriminate multiple degrees of freedom has shown great promise in the research literature, but it has yet to transition to a clinically viable option. This article describes the pertinent issues and best practices in EMG pattern recognition, identifies the major challenges in deploying robust control, and advocates research directions that may have an effect in the near future.
Ligand Binding and Functional Properties of Betaglycan, a Co-receptor of the Transforming Growth Factor-β Superfamily (2001)

Betaglycan, also known as the transforming growth factor-beta (TGF-beta) type III receptor, is a membrane-anchored proteoglycan that binds TGF-beta via its core protein. Deletion mutagenesis analysis has revealed two regions of betaglycan ectodomain capable of binding TGF-beta: one at the amino-terminal half, the endoglin-related region (López-Casillas, F., Payne, H., Andres, J. L., and Massagué, J. (1994) J. Cell Biol. 124, 557-568), and the other at the carboxyl-terminal half, the uromodulin-related region (Pepin, M.-C., Beauchemin, M., Plamondon, J., and O'Connor-McCourt, M. D. (1994) Proc. Natl. Acad. Sci. U. S. A 91, 6997-7001). In the present work we have functionally characterized these ligand binding regions. Similar to the wild type receptor, both regions bind TGF-beta2 with higher affinity than TGF-beta1. However, only the endoglin-related region increases the TGF-beta2 labeling of the TGF-beta type II receptor, the so-called "TGF-beta -presentation" function of the wild type receptor. Despite this preference, both regions as well as the wild type receptor mediate the TGF-beta2-dependent Smad2 phosphorylation, indicating that they can function indistinguishably as TGF-beta-enhancing co-receptors. On the other hand, we found that the recently described ability of the wild type betaglycan to bind inhibin A is a property of the core protein that resides in the uromodulin-related region. Binding competition experiments indicate that this region binds inhibin and TGF-beta with the following relative affinities: TGF-beta2 > inhibin A > TGF-beta1. All together, the present results suggest that betaglycan ectodomain is endowed with two bona fide independent ligand binding domains that can perform specialized functions as co-receptors of distinct members of the TGF-beta superfamily.
Magainins, a class of antimicrobial peptides from Xenopus skin: isolation, characterization of two active forms, and partial cDNA sequence of a precursor. (1987)

A family of peptides with broad-spectrum antimicrobial activity has been isolated from the skin of the African clawed frog Xenopus laevis. It consists of two closely related peptides that are each 23 amino acids and differ by two substitutions. These peptides are water soluble, nonhemolytic at their effective antimicrobial concentrations, and potentially amphiphilic. At low concentrations they inhibit growth of numerous species of bacteria and fungi and induce osmotic lysis of protozoa. The sequence of a partial cDNA of the precursor reveals that both peptides derive from a common larger protein. These peptides appear to represent a previously unrecognized class of vertebrate antimicrobial activities.