gebhart/patrepeval huggingface dataset:
Structure-Based Site of Metabolism Prediction for Cytochrome P450 2D6 (2011)

Realistic representation of protein flexibility in biomolecular simulations remains an unsolved fundamental problem and is an active area of research. The high flexibility of the cytochrome P450 2D6 (CYP2D6) active site represents a challenge for accurate prediction of the preferred binding mode and site of metabolism (SOM) for compounds metabolized by this important enzyme. To account for this flexibility, we generated a large ensemble of unbiased CYP2D6 conformations, to which small molecule substrates were docked to predict their experimentally observed SOM. SOM predictivity was investigated as a function of the number of protein structures, the scoring function, the SOM-heme cutoff distance used to distinguish metabolic sites, and intrinsic reactivity. Good SOM predictions for CYP2D6 require information from the protein. A critical parameter is the distance between the heme iron and the candidate site of metabolism. The best predictions were achieved with cutoff distances consistent with the chemistry relevant to CYP2D6 metabolism. Combination of the new ensemble-based docking method with estimated intrinsic reactivities of substrate sites considerably improved the predictivity of the model. Testing on an independent set of substrates yielded area under curve values as high as 0.93, validating our new approach.
Fully Integrated Glass Microfluidic Device for Performing High-Efficiency Capillary Electrophoresis and Electrospray Ionization Mass Spectrometry (2008)

A microfabricated device has been developed in which electrospray ionization is performed directly from the corner of a rectangular glass microchip. The device allows highly efficient electrokinetically driven separations to be coupled directly to a mass spectrometer (MS) without the use of external pressure sources or the insertion of capillary spray tips. An electrokinetic-based hydraulic pump is integrated on the chip that directs eluting materials to the monolithically integrated spray tip. A positively charged surface coating, PolyE-323, is used to prevent surface interactions with peptides and proteins and to reverse the electroosmotic flow in the separation channel. The device has been used to perform microchip CE-MS analysis of peptides and proteins with efficiencies over 200,000 theoretical plates (1,000,000 plates/m). The sensitivity and stability of the microfabricated ESI source were found to be comparable to that of commercial pulled fused-silica capillary nanospray sources.
A common pathway for T lymphocyte activation involving both the CD3-Ti complex and CD2 sheep erythrocyte receptor determinants. (1986)

T lymphocyte activation with monoclonal antibodies directed against the CD2 (T,p50) sheep red blood cell receptor antigen and against CD3 (T,p19,29) has been investigated. Co-stimulation of purified T lymphocytes with anti-CD3 (SP34) and anti-CD2 (9-1), which detects a unique epitope on the CD2 molecule, results in T cell activation and cell proliferation. Each antibody alone is unable to mediate this effect. Co-stimulation of purified T cells with two different anti-CD2 antibodies, 9-1 and 9.6, which detect two different epitopes on the CD2 molecule, are also mitogenic. In contrast, the combination of anti-CD3 (SP34) and anti-CD2 (9.6) cannot induce T cell activation. These data suggest that the CD2 epitope defined by the 9-1 antibody is functionally important for T cell activation via the CD3/Ti complex. Furthermore, it is demonstrated that anti-CD3 (SP34) induces epitopic modulation of the CD2 molecule, resulting in enhanced expression of the CD2, 9-1 epitope. This epitope modulation of the CD2 (9-1) epitope by anti-CD3 (SP34) occurs instantaneously at 4 degrees C and in the presence of NaN3. The functional interaction between CD3 and CD2 occurs in spite of any evidence of complex formation between these two molecules. These data suggest that the T cell differentiation antigens CD3 and CD2 are jointly involved in antigen-specific T cell activation. The data are consistent with a model for antigen-specific T cell activation involving both the CD3/Ti complex and subsequent activation of the CD2 complex T cell activation by co-stimulation with anti-CD3 (SP34) and anti-CD2 (9-1) is substantially enhanced by the addition of exogenous, purified interleukin 1 (IL 1). These data would suggest that the CD2 complex, as well as the putative IL 1 receptor, are involved in separate and complementary receptor-ligand interactions, resulting in the amplification of antigen-specific T cell responses.
A Novel Cancer Testis Antigen, A-Kinase Anchor Protein 4 (AKAP4) Is a Potential Biomarker for Breast Cancer (2013)

Collectively, our data suggests that AKAP4 may be used as serum based diagnostic test for an early detection and diagnosis of breast cancer and may be a potential target for immunotherapeutic use.
X linked exudative vitreoretinopathy: clinical features and genetic linkage analysis. (1993)

A four generation family in which familial exudative vitreoretinopathy is inherited as an X linked condition is described. Essentially the condition is one of abnormal vascularisation and signs at birth are those of a retinopathy superficially resembling retinopathy of prematurity, retinal folds, or, in advanced cases, enophthalmos or even phthisis. Prognosis depends on the progression of the retinal changes. The family members, including seven affected males and five obligate carrier females, have been types for 20 DNA markers, and linkage analysis suggests a gene locus either at Xq21.3 or at Xp11. As the latter region includes the locus for the gene for Norrie disease, it is possible that this and X linked vitreoretinopathy are allelic. We can further speculate that the differences in severity of the clinical manifestations are dependent only upon the timing of the insult.
Mitochondrial function in vivo evaluated by NADH fluorescence: from animal models to human studies (2006)

Normal mitochondrial function is a critical factor in maintaining cellular homeostasis in various organs of the body. Due to the involvement of mitochondrial dysfunction in many pathological states, the real-time in vivo monitoring of the mitochondrial metabolic state is crucially important. This type of monitoring in animal models as well as in patients provides real-time data that can help interpret experimental results or optimize patient treatment. The goals of the present review are the following: 1) to provide an historical overview of NADH fluorescence monitoring and its physiological significance; 2) to present the solid scientific ground underlying NADH fluorescence measurements based on published materials; 3) to provide the reader with basic information on the methodologies used in the past and the current state of the art fluorometers; and 4) to clarify the various factors affecting monitored signals, including artifacts. The large numbers of publications by different groups testify to the valuable information gathered in various experimental conditions. The monitoring of NADH levels in the tissue provides the most important information on the metabolic state of the mitochondria in terms of energy production and intracellular oxygen levels. Although NADH signals are not calibrated in absolute units, their trend monitoring is important for the interpretation of physiological or pathological situations. To understand tissue function better, the multiparametric approach has been developed where NADH serves as the key parameter. The development of new light sources in UV and visible spectra has led to the development of small compact units applicable in clinical conditions for better diagnosis of patients.
Visualizing enveloping layer glycans during zebrafish early embryogenesis (2010)

Developmental events can be monitored at the cellular and molecular levels by using noninvasive imaging techniques. Among the biomolecules that might be targeted for imaging analysis, glycans occupy a privileged position by virtue of their primary location on the cell surface. We previously described a chemical method to image glycans during zebrafish larval development; however, we were unable to detect glycans during the first 24 hours of embryogenesis, a very dynamic period in development. Here we report an approach to the imaging of glycans that enables their visualization in the enveloping layer during the early stages of zebrafish embryogenesis. We microinjected embryos with azidosugars at the one-cell stage, allowed the zebrafish to develop, and detected the metabolically labeled glycans with copper-free click chemistry. Mucin-type O-glycans could be imaged as early as 7 hours postfertilization, during the gastrula stage of development. Additionally, we used a nonmetabolic approach to label sialylated glycans with an independent chemistry, enabling the simultaneous imaging of these two distinct classes of glycans. Imaging analysis of glycan trafficking revealed dramatic reorganization of glycans on the second time scale, including rapid migration to the cleavage furrow of mitotic cells. These studies yield insight into the biosynthesis and dynamics of glycans in the enveloping layer during embryogenesis and provide a platform for imaging other biomolecular targets by microinjection of appropriately functionalized biosynthetic precursors.
Tissue Engineering: Orthopedic Applications (1999)

Because of an aging population and increased occurrence of sports-related injuries, musculoskeletal disorders have become one of the major health concerns in the United States. Current treatments, although fairly successful, do not provide the optimum therapy. These treatments typically rely on donor tissues obtained either from the patient or from another source. The former raises the issue of supply, whereas the latter poses the risk of rejection and disease transfer. This has prompted orthopedic surgeons and scientists to look for viable alternatives. In recent years, tissue engineering has gained increasing support as a method to treat orthopedic disorders. Because it uses principles of engineering, biology, and chemistry, tissue engineering may provide a more effective approach to the treatment of musculoskeletal disorders than traditional methods. This chapter presents a review of current methods and new tissue-engineering techniques for the treatment of disorders affecting bone, ligament, and cartilage.
The Effectiveness of Dams as a Sustainable Water Resource (2003)

Farm dams are a common sight on rural properties as an inexpensive water supply for stock or agribusiness. The magnitude of the losses from farm dams due to evaporation, leakage and seepage is illustrated. How these factors impact on the operation of the shallow pond as an effective method of water storage are discussed. The question is addressed on whether this farming practice is a sustainable and economic way of storing water. Some alternatives are explored for relative costs, efficiencies, quality of water stored, and impediments to implementation.
Shape‐Controlled Synthesis of Metal Nanostructures: The Case of Silver (2004)

The concept of shape-controlled synthesis is discussed by investigating the growth mechanisms for silver nanocubes, nanowires, and nanospheres produced through a polymer-mediated polyol process. Experimental parameters, such as the concentration of AgNO(3) (the precursor to silver), the molar ratio between poly(vinylpyrrolidone) (PVP, the capping agent) and AgNO(3), and the strength of chemical interaction between PVP and various crystallographic planes of silver, were found to determine the crystallinity of seeds (e.g., single crystal versus decahedral multiply twinned particles). In turn, the crystallinity of a seed and the extent of the PVP coverage on the seed were both instrumental in controlling the morphology of final product. The ability to generate silver nanostructures with well-defined morphologies provides a great opportunity to experimentally and systematically study the relationship between their properties and geometric shapes.
A robust digital image watermarking method using wavelet-based fusion (2002)

We present an approach for still image watermarking in which the watermark embedding process employs multiresolution fusion techniques and incorporates a model of the human visual system (HVS). The original unmarked image is required to extract the watermark. Simulation results demonstrate the high robustness of the algorithm to such image degradations as JPEG compression, additive noise and linear filtering.
Airway Management in Patients with Pierre Robin Syndrome (1966)

Atlanta, Georgia * Chief Anesthesiologist, Henrietta Egleston Hospital for Children, Atlanta, Georgia. William E. Schatten, M.D. 710 Peachtree Street Atlanta, Georgia 30308
Immune interferon enhances functional properties of human granulocytes: role of Fc receptors and effect of lymphotoxin, tumor necrosis factor, and granulocyte-macrophage colony-stimulating factor. (1987)

We report here a comparative study of the effects of several cytokines known to affect myeloid cell differentiation on functional properties of human mature granulocytes. We show that recombinant interferon-gamma (rIFN-gamma), recombinant granulocyte/macrophage-colony stimulating factor (rGM-CSF), recombinant tumor necrosis factor (rTNF), and lymphotoxin (LT) purified to homogeneity are potent stimulators of polymorphonuclear cells (PMN) activity. All cytokines enhance antibody-dependent cell-mediated cytotoxicity (Ab-CMC) mediated by human PMN; however, rGM-CSF, rTNF, and LT have an immediate and short-lived effect on the PMN, whereas the activation by rIFN-gamma requires several hours of induction but can be observed up to 24 to 48 hr of culture. Only the effect of rIFN-gamma is in part dependent on induction of a high-affinity FcR for monomeric IgG on PMN, as suggested by two-color sorting analysis, and on mechanisms that result in prolonged survival of PMN in a functionally active state to mediate oxidative burst, phagocytosis, and bactericidal activity. Greater enhancement of Ab-CMC is obtained by using rIFN-gamma in combination with the other cytokines. Our data indicate that cytokines previously defined on the basis of their cytotoxic effects mediate a wide spectrum of activities on mature myeloid cells and provide evidence for their possible role in vivo, alone or in combination with rIFN-gamma, in modulating functional activities of cells responsible for non-adaptive systems of defense.
Graphene-Like Two-Dimensional Materials (2013)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTGraphene-Like Two-Dimensional MaterialsMingsheng Xu*, Tao Liang, Minmin Shi, and Hongzheng ChenView Author Information State Key Laboratory of Silicon Materials, MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, People's Republic of China*Address: Department of Polymer Science and Engineering, Zhejiang University, #38 Zheda Road, Hangzhou 310027, China. E-mail: [email protected]Cite this: Chem. Rev. 2013, 113, 5, 3766–3798Publication Date (Web):January 3, 2013Publication History Received1 July 2012Published online3 January 2013Published inissue 8 May 2013https://pubs.acs.org/doi/10.1021/cr300263ahttps://doi.org/10.1021/cr300263areview-articleACS PublicationsCopyright © 2013 American Chemical SocietyRequest reuse permissionsArticle Views78554Altmetric-Citations3763LEARN 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:Electrical conductivity,Layers,Monolayers,Silicon,Two dimensional materials Get e-Alerts
Anti-CD117 antibody depletes normal and myelodysplastic syndrome human hematopoietic stem cells in xenografted mice (2019)

The myelodysplastic syndromes (MDS) represent a group of clonal disorders that result in ineffective hematopoiesis and are associated with an increased risk of transformation into acute leukemia. MDS arises from hematopoietic stem cells (HSCs); therefore, successful elimination of MDS HSCs is an important part of any curative therapy. However, current treatment options, including allogeneic hematopoietic cell transplantation (HCT), often fail to ablate disease-initiating MDS HSCs, and thus have low curative potential and high relapse rates. Here, we demonstrate that human HSCs can be targeted and eliminated by monoclonal antibodies (mAbs) that bind cell-surface CD117 (c-Kit). We show that an anti-human CD117 mAb, SR-1, inhibits normal cord blood and bone marrow HSCs in vitro. Furthermore, SR-1 and clinical-grade humanized anti-human CD117 mAb, AMG 191, deplete normal and MDS HSCs in vivo in xenograft mouse models. Anti-CD117 mAbs also facilitate the engraftment of normal donor human HSCs in MDS xenograft mouse models, restoring normal human hematopoiesis and eradicating aggressive pathologic MDS cells. This study is the first to demonstrate that anti-human CD117 mAbs have potential as novel therapeutics to eradicate MDS HSCs and augment the curative effect of allogeneic HCT for this disease. Moreover, we establish the foundation for use of these antibody agents not only in the treatment of MDS but also for the multitude of other HSC-driven blood and immune disorders for which transplant can be disease-altering.
Standard Operating Procedures for Serum and Plasma Collection: Early Detection Research Network Consensus Statement Standard Operating Procedure Integration Working Group (2008)

Specimen collection is an integral component of clinical research. Specimens from subjects with various stages of cancers or other conditions, as well as those without disease, are critical tools in the hunt for biomarkers, predictors, or tests that will detect serious diseases earlier or more readily than currently possible. Analytic methodologies evolve quickly. Access to high-quality specimens, collected and handled in standardized ways that minimize potential bias or confounding factors, is key to the "bench to bedside" aim of translational research. It is essential that standard operating procedures, "the how" of creating the repositories, be defined prospectively when designing clinical trials. Small differences in the processing or handling of a specimen can have dramatic effects in analytical reliability and reproducibility, especially when multiplex methods are used. A representative working group, Standard Operating Procedures Internal Working Group (SOPIWG), comprised of members from across Early Detection Research Network (EDRN) was formed to develop standard operating procedures (SOPs) for various types of specimens collected and managed for our biomarker discovery and validation work. This report presents our consensus on SOPs for the collection, processing, handling, and storage of serum and plasma for biomarker discovery and validation.
Specific Redistribution of Cell-Penetrating Peptides from Endosomes to the Cytoplasm and Nucleus upon Laser Illumination (2004)

Cell-penetrating peptides (CPPs), once postulated to cross cell membranes in a non-endocytic, non-energy-dependent process, have since been found to accumulate in vesicles in live mammalian cells. In this study, we show that it is possible to use laser light from a confocal microscope to cause labeled peptide-conjugated CPPs to redistribute from vesicles into the cytoplasm and nucleus of cells. Following redistribution, the cells are found to be biologically responsive, and they retain morphology for several hours. It was possible to initiate redistribution of both fluorescein- and Alexa633-labeled peptides by selective irradiation of one of the fluorophores. These peptides could potentially be used as tracers to selectively deliver cargo biomolecules into cells by laser illumination using a standard fluorescence confocal microscope.
Dual Inhibition of β-Adrenergic and Angiotensin II Receptors by a Single Antagonist (2003)

We show that direct interactions between betaARs and AT1Rs may have profound consequences on the overall response to drugs that antagonize these receptors.
Studies of molybdenum compounds. 6. Diaryl(2,2'-bipyridyl)dioxomolybdenum(VI) and related compounds (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies of molybdenum compounds. 6. Diaryl(2,2'-bipyridyl)dioxomolybdenum(VI) and related compoundsG. N. Schrauzer, Xumu. Zhang, Nanhui. Liu, and E. O. SchlemperCite this: Organometallics 1988, 7, 2, 279–282Publication Date (Print):February 1, 1988Publication History Published online1 May 2002Published inissue 1 February 1988https://pubs.acs.org/doi/10.1021/om00092a007https://doi.org/10.1021/om00092a007research-articleACS PublicationsRequest reuse permissionsArticle Views126Altmetric-Citations18LEARN 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
Molecular and Cellular Aspects of the Insulin-Like Growth Factor I Receptor (1995)

THE insulin-like growth factors (IGFs) and their receptors and binding proteins constitute a family of cellular modulators that play essential roles in the regulation of growth and development. The IGF ligands include three structurally related peptides: insulin, IGF-I, and IGF-II. Unlike insulin, IGF-I and IGF-II are expressed ubiquitously, albeit in a highly regulated manner (see reviews in Refs. 1-5). The biological functions of the IGFs are mediated by a family of transmembrane receptors, which includes the insulin, IGF-I, and IGF-II/mannose-6-phosphate (M-6-P) receptors. While the IGF-I receptor is the primary mediator of IGF action, the insulin and IGF-II/M-6-P receptors may also mediate some of these functions (Fig. 1) (6, 7). The biological actions of the IGFs are modulated by a family of at least six IGF-binding proteins (IGFBPs) that are found in the circulation and in extracellular compartments and are produced by most tissues. The IGFBPs are capable of inhibiting or enhancing IGF effects and may even have ligand-independent effects (see reviews in Refs. 8–11). This review will focus on the IGF-I receptor and will discuss various aspects of its molecular structure and the cellular effects elicited by its activation.