gebhart/patrepeval huggingface dataset:
Sequence of the D-aspartyl/L-isoaspartyl protein methyltransferase from human erythrocytes (1989)

A widely distributed protein methyltransferase catalyzes the transfer of a methyl group from S-adenosyl-methionine to the free carboxyl groups of D-aspartyl and/or L-isoaspartyl derivatives of L-aspartyl and L-asparaginyl residues. This enzyme has been postulated to function in the repair or the catabolism of age-damaged proteins. We present here the complete amino acid sequence of the more basic isozyme I of this enzyme from human erythrocytes. The sequence was determined by Edman degradation and mass spectral analysis of overlapping trypsin, Staphylococcus aureus V8 protease, Pseudomonas fragi endoproteinase Asp-N, cyanogen bromide, and hydroxylamine-generated fragments. The NH2-terminus is modified by acetylation and the protein contains 226 amino acids for a calculated molecular weight of 24,575. This value is in good agreement with the molecular weight determined for the purified protein by polyacrylamide gel electrophoresis in the presence of dodecyl sulfate and by gel filtration chromatography under nondenaturing conditions. The identification of 2 different amino acid residues at both positions 22 and 119 may indicate the presence of allelic variants or of two or more closely related structural genes. Finally, comparison of this sequence with those of methyltransferases for RNA, DNA, and small molecules, as well as other S-adenosylmethionine-utilizing enzymes, shows that many of these proteins share elements of three regions of sequence similarity and may be structurally or evolutionarily related.
Photocleavage of Peptides and Oligodeoxynucleotides Carrying 2‐Nitrobenzyl Groups (2009)

Abstract magnified image Peptides and oligodeoxynucleotides containing photolabile 2‐nitrobenzyl groups as mid‐sequences were prepared. Photocleavage of aqueous solutions of these compounds neared completion within 30 min to a few hours depending on the photolabile group used. A photolabile group was introduced in the loop of an intramolecular oligodeoxynucleotide hairpin. Melting curves of the hairpin with and without the complementary oligodeoxynucleotide showed a preference for the intramolecular hairpin form, but an intermolecular duplex was observed after photolysis. These results open the possibility of using photolabile DNA hairpins for the fabrication of patterned surfaces.
On the Synthesis of Phosphonamidate Peptides (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOn the Synthesis of Phosphonamidate PeptidesHans-Juergen Musiol, Frank Grams, Sabine Rudolph-Boehner, and Luis MoroderCite this: J. Org. Chem. 1994, 59, 21, 6144–6146Publication Date (Print):October 1, 1994Publication History Published online1 May 2002Published inissue 1 October 1994https://pubs.acs.org/doi/10.1021/jo00100a007https://doi.org/10.1021/jo00100a007research-articleACS PublicationsRequest reuse permissionsArticle Views369Altmetric-Citations29LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Pheromone Response in Yeast (1992)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Controlling potassium channel activities: Interplay between the membrane and intracellular factors (2001)

Neural signaling is based on the regulated timing and extent of channel opening; therefore, it is important to understand how ion channels open and close in response to neurotransmitters and intracellular messengers. Here, we examine this question for potassium channels, an extraordinarily diverse group of ion channels. Voltage-gated potassium (Kv) channels control action-potential waveforms and neuronal firing patterns by opening and closing in response to membrane-potential changes. These effects can be strongly modulated by cytoplasmic factors such as kinases, phosphatases, and small GTPases. A Kv alpha subunit contains six transmembrane segments, including an intrinsic voltage sensor. In contrast, inwardly rectifying potassium (Kir) channels have just two transmembrane segments in each of its four pore-lining alpha subunits. A variety of intracellular second messengers mediate transmitter and metabolic regulation of Kir channels. For example, Kir3 (GIRK) channels open on binding to the G protein betagamma subunits, thereby mediating slow inhibitory postsynaptic potentials in the brain. Our structure-based functional analysis on the cytoplasmic N-terminal tetramerization domain T1 of the voltage-gated channel, Kv1.2, uncovered a new function for this domain, modulation of voltage gating, and suggested a possible means of communication between second messenger pathways and Kv channels. A yeast screen for active Kir3.2 channels subjected to random mutagenesis has identified residues in the transmembrane segments that are crucial for controlling the opening of Kir3.2 channels. The identification of structural elements involved in potassium channel gating in these systems highlights principles that may be important in the regulation of other types of channels.
Prader-Willi syndrome: reflections on seminal studies and future therapies (2020)

Prader-Willi syndrome (PWS) is caused by the loss of function of the paternally inherited 15q11-q13 locus. This region is governed by genomic imprinting, a phenomenon in which genes are expressed exclusively from one parental allele. The genomic imprinting of the 15q11-q13 locus is established in the germline and is largely controlled by a bipartite imprinting centre. One part, termed the Prader-Willi syndrome imprinting center (PWS-IC), comprises a CpG island that is unmethylated on the paternal allele and methylated on the maternal allele. The second part, termed the Angelman syndrome imprinting centre, is required to silence the PWS_IC in the maternal germline. The loss of the paternal contribution of the imprinted 15q11-q13 locus most frequently occurs owing to a large deletion of the entire imprinted region but can also occur through maternal uniparental disomy or an imprinting defect. While PWS is considered a contiguous gene syndrome based on large-deletion and uniparental disomy patients, the lack of expression of only non-coding RNA transcripts from the <i>SNURF-SNRPN/SNHG14</i> may be the primary cause of PWS. Patients with small atypical deletions of the paternal <i>SNORD116</i> cluster alone appear to have most of the PWS related clinical phenotypes. The loss of the maternal contribution of the 15q11-q13 locus causes a separate and distinct condition called Angelman syndrome. Importantly, while much has been learned about the regulation and expression of genes and transcripts deriving from the 15q11-q13 locus, there remains much to be learned about how these genes and transcripts contribute at the molecular level to the clinical traits and developmental aspects of PWS that have been observed.
Controlled and automatic human information processing: II. Perceptual learning, automatic attending and a general theory. (1977)

Tested the 2-process theory of detection, search, and attention presented by the current authors (1977) in a series of experiments. The studies (a) demonstrate the qualitative difference between 2 modes of information processing: automatic detection and controlled search; (b) trace the course of the
Reprogramming nuclei: insights from cloning, nuclear transfer and heterokaryons (2000)

Mammals and amphibians can be cloned following the transfer of embryonic nuclei into enucleated eggs or oocytes. As nuclear functions become more specialized in the differentiated cells of an adult, successful cloning using these nuclei as donors becomes more difficult. Differentiation involves the assembly of specialized forms of repressive chromatin including linker histones, Polycomb group proteins and methyl-CpG-binding proteins. These structures compartmentalize chromatin into functional domains and maintain the stability of the differentiated state through successive cell divisions. Efficient cloning requires the erasure of these structures. The erasure can be accomplished through use of molecular chaperones and enzymatic activities present in the oocyte, egg or zygote. We discuss the mechanisms involved in reprogramming nuclei after nuclear transfer and compare them with those that occur during remodeling of somatic nuclei after heterokaryon formation. Finally we discuss how one might alter the properties of adult nuclei to improve the efficiency of cloning.
Multi-dimensional velocity estimation with ultrasound using spatial quadrature (1998)

Conventional ultrasonic motion or flow velocity estimation is limited to the axial velocity component. A novel technique, called "spatial quadrature," for the simultaneous estimation of axial and lateral velocity components is introduced. This technique utilizes even and odd spatial weightings of the point spread function that have a quandrature relationship. These weightings produce modulation in the received echo that can be decoded to quantify lateral motion. This estimator can be implemented for two-dimensional velocity estimation with a conventional transducer array and medical ultrasound scanner, preferably one with parallel receive processing. The technique also can be extended to three-dimensional velocity estimation given an appropriate 2-D transducer and scanner architecture. Discussed are space and frequency domain descriptions of this estimator in the context of a brief overview of 2-D flow estimation methods, including analyses characterizing the performance envelope of this estimator. In addition, the application of this technique in CW and PW regimes, and with both radio frequency and baseband quadrature (I- and-Q) data, are discussed. Phantom studies demonstrate spatial quadrature in 2-D using a clinical scanner.
Infrared Laser Therapy for Ischemic Stroke: A New Treatment Strategy (2007)

The NEST-1 study indicates that infrared laser therapy has shown initial safety and effectiveness for the treatment of ischemic stroke in humans when initiated within 24 hours of stroke onset. A larger confirmatory trial to demonstrate safety and effectiveness is warranted.
Drug Absorption by the Respiratory Mucosa: Cell Culture Models and Particulate Drug Carriers (2002)

The inhalation route is of increasing interest for both local and systemic drug delivery, including macromolecular biopharmaceuticals, such as peptides, proteins, and gene therapeutics. In addition to appropriate aerosolization for deposition in relevant areas of the respiratory tract, therapeutic molecules may require an advanced carrier system for safe and efficient delivery to their target. Two approaches to obtain novel carrier systems for pulmonary drug delivery are large porous microparticles with a low aerodynamic diameter and lectin-functionalized liposomes. Epithelial cells of alveolar or bronchial origin, obtained either from patient material or from established cell lines, can be grown on permeable filter supports, resulting in polarized monolayers with functional intercellular junctions. With such in vitro models, transport of drugs into pulmonary epithelial cells and/or across the air-blood barrier, as well as the effect and efficacy of novel drug carrier systems can be systematically studied.
Host genetic mechanism of resistance and susceptibility to a bovine retroviral infection (1994)

Abstract The bovine leukemia virus (BLV) has approximately 50% nucleotide sequence similarity to HTLV types I and II, and shares common regulatory mechanisms, but differs in host cell tropism, with B‐cells comprising the primary target of infection. We have shown that progression of BLV infection to persistent lymphocytosis (PL) is under the control of the bovine major histocompatibility complex, mapping closest to BoLA class II genes. We recently narrowed the association to exon 2 of the BoLA‐DRB3 gene. This exon was cloned from animals with BoLA haplotypes previously found to be associated with resistance and susceptibility to PL. Sequence analysis revealed the presence of the amino acids Glu‐Arg (ER) at putative antigen binding residues 70 and 71 only in BoLA haplotypes associated with resistance. This correlation was confirmed in a case‐control study using an allele‐specific polymerase chain reaction for the detection of the ER motif at residues 70‐71. Analysis of infection in peripheral blood leukocytes by a new single cell detection methodology revealed that BLV‐infected PL‐resistant animals have fewer infected peripheral cells than age‐matched susceptible cows. These results provide a molecular basis for Ir gene control of resistance and susceptibility to PL and suggest that the cellular immune response is important in preventing the in vivo spread of BLV infection.
HERC2/USP20 coordinates CHK1 activation by modulating CLASPIN stability (2014)

CLASPIN is an essential mediator in the DNA replication checkpoint, responsible for ATR (ataxia telangiectasia and Rad3-related protein)-dependent activation of CHK1 (checkpoint kinase 1). Here we found a dynamic signaling pathway that regulates CLASPIN turn over. Under unperturbed conditions, the E3 ubiquitin ligase HERC2 regulates the stability of the deubiquitinating enzyme USP20 by promoting ubiquitination-mediated proteasomal degradation. Under replication stress, ATR-mediated phosphorylation of USP20 results in the disassociation of HERC2 from USP20. USP20 in turn deubiquitinates K48-linked-polyubiquitinated CLASPIN, stabilizing CLASPIN and ultimately promoting CHK1 phosphorylation and CHK1-directed checkpoint activation. Inhibition of USP20 expression promotes chromosome instability and xenograft tumor growth. Taken together, our findings demonstrated a novel function of HERC2/USP20 in coordinating CHK1 activation by modulating CLASPIN stability, which ultimately promotes genome stability and suppresses tumor growth.
A Nanofountain Probe with Sub‐100 nm Molecular Writing Resolution (2005)

Just the tip of the iceberg? The Nanofountain Probe (NFP) has been developed to produce molecular patterning at the sub-100 nm scale. In conjunction with an atomic force microscope probe, the volcano-shaped tip (shown in the SEM image) ensures controlled ink delivery from an on-chip reservoir to provide high-resolution patterning for manifold potential applications.
Molecular Cloning of Mouse Alpha-1,6-Fucosyltransferase and Expression of Its mRNA in the Developing Cerebrum (2000)

Complementary DNA encoding mouse alpha-1,6-fucosyltransferase (FUT) was cloned. The deduced primary structure consisted of 575 amino acids and had 96.0% and 93.0% identity with alpha-1,6-FUT of human and porcine origin, respectively. Quantitative analysis of alpha-1,6-FUT mRNA expression during selected developmental stages of the cerebrum showed that the expression increased during later embryonic stages and was highest in the early postnatal stages (P1 to P7), after which it declined somewhat but still remained relatively high in the mature adult. The expression profile suggests important roles of FUT in the developing central nervous system.
Tissue Specificity of Decellularized Rhesus Monkey Kidney and Lung Scaffolds (2013)

Initial steps in establishing an optimal strategy for functional bioengineered tissues is generation of three-dimensional constructs containing cells with the appropriate organization and phenotype. To effectively utilize rhesus monkey decellularized kidney scaffolds, these studies evaluated two key parameters: (1) residual scaffold components after decellularization including proteomics analysis, and (2) the use of undifferentiated human embryonic stem cells (hESCs) for recellularization in order to explore cellular differentiation in a tissue-specific manner. Sections of kidney and lung were selected for a comparative evaluation because of their similar pattern of organogenesis. Proteomics analysis revealed the presence of growth factors and antimicrobial proteins as well as stress proteins and complement components. Immunohistochemistry of recellularized kidney scaffolds showed the generation of Cytokeratin+ epithelial tubule phenotypes throughout the scaffold that demonstrated a statistically significant increase in expression of kidney-associated genes compared to baseline hESC gene expression. Recellularization of lung scaffolds showed that cells lined the alveolar spaces and demonstrated statistically significant upregulation of key lung-associated genes. However, overall expression of kidney and lung-associated markers was not statistically different when the kidney and lung recellularized scaffolds were compared. These results suggest that decellularized scaffolds have an intrinsic spatial ability to influence hESC differentiation by physically shaping cells into tissue-appropriate structures and phenotypes, and that additional approaches may be needed to ensure consistent recellularization throughout the matrix.
Stroke rehabilitation: analysis of repeated Barthel index measures. (1979)

Functional abilities of stroke patients in a rehabilitation hospital are recorded every 2 weeks using the Barthel index. For purposes of this study, data were collected retrospectively and prospectively from consecutive records according to predetermined criteria on forms coded for computer analysis. Total scores of 110 patients were correlated with length of stay, placement at discharge and scores in individual functional abilities. Analysis of the data reveals that an initial score over 40 on the Barthel index defines a population with a greater proportion of discharges to home and that patients with initial scores over 60 have a shorter length of stay. Further analysis indicates a predictable progression in the development of functional skills in this population so that with a Barthel score below 40, no one was independent in the mobility skills and fewer than 50% were independent in the very basic skills, such as feeding, grooming and sphincter control. A score of 60 appears to be a pivotal score where patients move from dependency to assisted independence.
The Phosphorus Aspects of Green Chemistry: the Use of Quaternary Phosphonium Salts and 1,3-Dialkylimidazolium Hexafluorophosphates in Organic Synthesis (2006)

The search for suitable ionic liquids that are non-volatile, non-toxic, dissolve a variety of reactants and are recyclable is a real challenge for chemists to be able to replace the traditional solvents that are volatile, flammable and toxic. This segment of chemistry has, these days, become a firm part of green chemistry attracting much attention. The present review summarizes and critically discusses the data accumulated in recent years on the synthesis and utilization of phosphorus containing ionic liquids, such as imidazolium hexafluorophosphates and phosphonium salts. As regards the preparation of ionic liquids, the key steps are quaternization and the introduction of the corresponding anion. Physical properties of the ionic liquids can be fine-tuned by selecting suitable cation-anion pairs. The reactions studied in ionic liquids embraces catalytic hydrogenations, transfer hydrogenations, oxidations, hydroformylations, carbonylations, alkylations, acylations, nucleophilic substitutions, halogenations, condensations, Diels-Alder reactions, Michael additions, coupling reactions and transformations in organophosphorus chemistry. Ionic liquids are especially suitable to accommodate catalytic reactions where one of the components is a gas. Stress was laid to highlight the chemo-, regio-, diastereo- and, especially, the enantioselectivity of the reactions performed in ionic liquids. The data on the ecotoxicity of imidazolium hexafluorophosphates and phosphonium salts are briefly discussed. Keywords: Phosphonium Salts, Nucleophilic substitutions, Hydrogenations, asymmetric epoxidation, Carbonylations
A multiscale approach to pixel-level image fusion (2005)

Pixel level image fusion refers to the processing and synergistic combination of information gathered by various imaging sources to provide a better understanding of a scene. We formulate the image fusion as an optimization problem and propose an inf
OpenFace: An open source facial behavior analysis toolkit (2016)

Over the past few years, there has been an increased interest in automatic facial behavior analysis and understanding. We present OpenFace - an open source tool intended for computer vision and machine learning researchers, affective computing community and people interested in building interactive applications based on facial behavior analysis. OpenFace is the first open source tool capable of facial landmark detection, head pose estimation, facial action unit recognition, and eye-gaze estimation. The computer vision algorithms which represent the core of OpenFace demonstrate state-of-the-art results in all of the above mentioned tasks. Furthermore, our tool is capable of real-time performance and is able to run from a simple webcam without any specialist hardware. Finally, OpenFace allows for easy integration with other applications and devices through a lightweight messaging system.
Identification of AF17 as a downstream gene of the beta-catenin/T-cell factor pathway and its involvement in colorectal carcinogenesis. (2001)

To elucidate the molecular mechanism of colorectal carcinogenesis, we have been attempting to isolate genes involved in the beta-catenin/T-cell factor pathway. In the experiments reported here, analysis by cDNA microarray indicated that AF17, a fusion partner of the MLL gene in acute leukemias with t(11;17)(q23;q21), was transactivated according to accumulation of beta-catenin. Expression of AF17 was significantly enhanced in 8 of the 12 colorectal cancer tissues examined. Introduction of a plasmid designed to express AF17 stimulated growth of NIH3T3 cells, and fluorescence-activated cell sorter analysis indicated that the AF17 regulation of cell-cycle progression was occurring mainly at the G(2)-M transition. Our results suggest that the AF17 gene product is likely to be involved in the beta-catenin-T-cell factor/lymphoid enhancer factor signaling pathway and to function as a growth-promoting, oncogenic protein. These findings should aid development of new strategies for diagnosis, treatment, and prevention of colon cancers and acute leukemias by clarifying the pathogenesis of these conditions.