gebhart/patrepeval huggingface dataset:
Participation of Cytochrome b5 in CMP-N- Acetylneuraminic Acid Hydroxylation in Mouse Liver Cytosol1 (1990)

The activity of CMP-N-acetylneuraminic acid hydroxylase, that converts CMP-N-acetylneuraminic acid (CMP-NeuAc) to CPM-N-glycolylneuraminic acid (CMP-NeuGc), in mouse liver was determined by a newly developed HPLC method using non-radioactive CMP-NeuAc as a substrate. The activity was detected in the cytosol fraction but not in the microsomal fraction. Either NADH or NADPH was used as an electron donor by the cytosol enzyme, but NADH was much more efficiently used than NADPH. An antibody against cytochrome b5 markedly reduced the CMP-NeuAc hydroxylase activity when added to incubation mixture containing either NADH or NADPH as an electron donor. These data led us to postulate the following electron transport system, which is involved in the CMP-NeuAc hydroxylation in mouse liver cytosol: (formula; see text) where X, Y, and Z are components supposedly involved.
Functional mapping of the FcγRII binding site on human IgG1 by synthetic peptides (2004)

Receptors specific for the Fc part of IgG (Fc gamma R) are expressed by several cell types and play diverse roles in immune responses. Impaired function of the activating and inhibitory Fc gamma R may result in autoimmunity. Thus, the modulation of IgG-Fc gamma R interaction can be a target for the development of treatments for some autoimmune and inflammatory diseases. This study addresses the localization and functional characterization of linear sequences in human IgG1 which bind to Fc gamma RII. Peptides with overlapping sequences derived from the CH2 domain of human IgG1 between P(234) and S(298) were synthesized and used in binding and functional experiments. Binding of the peptides to Fc gamma R was assayed in vitro and ex vivo, and peptides found to interact were functionally tested. The shortest effective peptide was T(256)-P(271), which bound to soluble recombinant Fc gamma RIIb with K(d)=6 x 10(6) M(-1). The biotinylated peptides R(255)-P(271) and T(256)-P(271) complexed by avidin exhibited functional activity; they induced Fc gamma RIIb-mediated inhibition of the BCR-triggered Ca(2+) response of human Burkitt lymphoma cells, and inflammatory cytokine production (TNF-alpha and IL-6) by the human monocyte cell line MonoMac. In conclusion, our results suggest that the selected peptides functionally represent the Fc gamma RII-binding part of IgG1.
Statistical timing analysis with path reconvergence and spatial correlations (2006)

State of the art statistical timing analysis (STA) tools often yield less accurate results when timing variables become correlated. Spatial correlation and correlation caused by path reconvergence are among those which are most difficult to deal with. Existing methods treating these correlations will either suffer from high computational complexity or significant errors. In this paper, we present a sensitivity pruning method which significantly reduces the computational cost to consider path reconvergence correlation. We also develop an accurate and efficient model to deal with the spatial correlation.
A Bcl-2 homolog encoded by Kaposi sarcoma-associated virus, human herpesvirus 8, inhibits apoptosis but does not heterodimerize with Bax or Bak (1997)

The Bcl-2 protein family is characterized by the ability to modulate cell death, and members of this family share two highly conserved domains called Bcl-2 homology 1 (BH1) and 2 (BH2) which have been shown to be critical for the death-repressor activity of Bcl-2 and Bcl-xL. Through sequence analysis we identified a novel viral Bcl-2 homolog, designated KSbcl-2, from human herpesvirus 8 (HHV8) or Kaposi sarcoma-associated herpesvirus. The overall amino acid sequence identity between KSbcl-2 and other Bcl-2 homologs is low (15-20%) but concentrated within the BH1 and BH2 regions. Overexpression of KSbcl-2 blocked apoptosis as efficiently as Bcl-2, Bcl-xL, or another viral Bcl-2 homolog encoded by Epstein-Barr virus, BHRF1. Interestingly, KS-bcl-2 neither homodimerizes nor heterodimerizes with other Bcl-2 family members, suggesting that KSbcl-2 may have evolved to escape any negative regulatory effects of the cellular Bax and Bak proteins. Furthermore, the herpesvirus Bcl-2 homologs including KSbcl-2, BHRF1, and ORF16 of herpesvirus saimiri contain poorly conserved Bcl-2 homology 3 (BH3) domains compared with other mammalian Bcl-2 homologs, implying that BH3 may not be essential for anti-apoptotic function. This is consistent with our observation that amino acid substitutions within the BH3 domain of Bcl-xL had no effect on its death-suppressor activity.
CD146 is a potential marker for the diagnosis of malignancy in cervical and endometrial cancer (2013)

Cluster of differentiation 146 (CD146) is an endothelial cell adhesion molecule which is overexpressed in various types of malignant cancer, including ovarian cancer. However, whether CD146 is overexpressed in another two types of gynecological cancer, cervical cancer and endometrial cancer, remains unclear. In the present study, we showed that CD146 expression levels were higher in cells from cervical cancer and endometrial cancer compared with their corresponding normal tissues, using anti-CD146 mouse antibody AA4 (mAb AA4) and that mAb AA4 exhibited a high performance for specificity, sensitivity and positive predictive value in the detection of these two types of cancer. CD146 expression was positively and significantly correlated with the pathological subtype of cervical cancer and with the histological grade and depth of myometrial invasion in endometrial cancer. In addition, we confirmed that CD146 is present in the majority of blood vessels in cervical and endometrial cancer, suggesting that CD146 may be actively implicated in the metastasis of cervical and endometrial cancer via the vascular system. Thus, this study provides insights for further development of CD146 mAb in the detection of gynecological malignant cancer types and implies that a combined treatment strategy of anti-CD146 immunotherapy with other traditional chemo- or radiotherapy treatments may be a promising approach against cervical and endometrial cancer.
Surfactant Promoted Enhancement in Electrochemical and Electrochromic Properties of Films of Prussian Blue and Its Analogs (1999)

The present study focuses attention on the effect of surfactants on modified electrodes with molecules of prussian blue and its analogs, which possess one or more redox centers and offer themselves as model surface systems for investigating surface effects. Among the surfactants studied the cationic surfactant cetyl trimethyl ammonium bromide has offered enhanced film growth and excellent electrochemical reversibility in addition to perceptible changes in electrochromic performance of the chosen model systems. Current‐time transients and visible absorption spectral data are presented to supplement and substantiate the enhanced effects. © 1999 The Electrochemical Society. All rights reserved.
Preparation and Properties of Oligodeoxynucleotides Containing 5-Iodouracil and 5-Bromo- and 5-Iodocytosine (1997)

The behavior of oligonucleotides containing 5-iodouracil, 5-bromocytidine, and 5-iodocytidine in concentrated ammonia is described. 5-Aminouracil and 5-aminocytidine are obtained as side products when deprotection is performed at 60 degrees C. Small amounts, if any, of side products are obtained when ammonia deprotection is performed at room temperature. The base-pairing properties of these 5-halopyrimidines including triple helix are described.
Unitary peak power reduction in multiple transmit antennas (2008)

This paper proposes a new peak-to-average power ratio (PAPR) reduction scheme in multiple transmit antenna environments. Instead of applying individual PAPR reduction on each antenna, a joint PAPR reduction technique is proposed. By applying a relevant unitary rotation over the transmit antennas, overall PAPR of the multiple transmit antenna system is reduced. This scheme does not require any side information to decode the signal in the receiver, enabling throughput-lossless PAPR reduction. Furthermore, there is no increase in the complexity of the receiver.
Innate and Adaptive Responses to Heat Shock Proteins in Behcet’s Disease (2013)

Behcet's disease (BD) is a systemic, chronic inflammatory disorder with both innate and adaptive immune responses. Heat shock proteins (HSP) are highly conserved molecules in different species with scavenger activity and involved in correct folding of newly synthesized proteins. T and B cell responses against HSPs are observed in BD patients in both αβ and γδ T-cell populations. 60-kD HSP (HSP60) is also shown to be recognized by pattern recognition receptors such as toll-like receptors (TLR) and is suggested to be an endogenous "danger" signal to the immune system with rapid inflammatory cytokine releases and enhancement of adaptive Th1-type responses. Elucidating the exact role of HSPs in BD pathogenesis might pave the way to less toxic therapeutic approaches to BD, such as antibacterial therapies and immunomodulation.
Single-Qubit Lasing and Cooling at the Rabi Frequency (2008)

For a superconducting qubit driven to perform Rabi oscillations and coupled to a slow electromagnetic or nanomechanical oscillator we describe previously unexplored quantum optics effects. When the Rabi frequency is tuned to resonance with the oscillator, the latter can be driven far from equilibrium. Blue detuned driving leads to a population inversion in the qubit and a bistability with lasing behavior of the oscillator; for red detuning the qubit cools the oscillator. This behavior persists at the symmetry point where the qubit-oscillator coupling is quadratic and decoherence effects are minimized. There the system realizes a "single-atom-two-photon laser."
Heterogeneous Three-Dimensional Electronics by Use of Printed Semiconductor Nanomaterials (2006)

We developed a simple approach to combine broad classes of dissimilar materials into heterogeneously integrated electronic systems with two- or three-dimensional layouts. The process begins with the synthesis of different semiconductor nanomaterials, such as single-walled carbon nanotubes and single-crystal micro- and nanoscale wires and ribbons of gallium nitride, silicon, and gallium arsenide on separate substrates. Repeated application of an additive, transfer printing process that uses soft stamps with these substrates as donors, followed by device and interconnect formation, yields high-performance heterogeneously integrated electronics that incorporate any combination of semiconductor nanomaterials on rigid or flexible device substrates. This versatile methodology can produce a wide range of unusual electronic systems that would be impossible to achieve with other techniques.
Retinal prosthesis device based on pulse-frequency-modulation vision chip (2005)

We describe a retinal prosthesis device that uses an image sensor based on a pulse frequency modulation (PFM) photosensor array. A PFM-based photosensor converts light intensity into the frequency of an output electrical pulse stream, and thus is suitable for stimulating retinal cells. We demonstrate various circuit improvements for image preprocessing and packaging techniques and present the results of an electrophysiology experiment.
Restenosis after Angioplasty (1993)

Restenosis after angioplasty occurs in 30-50% of patients, and a repeat procedure is necessary in 20% within 6 mon. Over the last 10 yr, numerous drugs have been evaluated to reduce this problem. Although none have proven successful, an improved understanding of the pathophysiology, pharmacology, and clinical trial design has resulted. Current approaches to the problem include the use of combination drug therapy, local delivery at site of injury, and use of highly specific drugs including local gene therapy. (Cardiol Rev 1993;1:4, 209-217)
Elaboration and Characterization of Phospholipid Langmuir−Blodgett Films (1996)

In order to model biological membranes, DPPE (1,2-dihexadecanoyl-sn-glycero-3-phosphoethanolamine) and DPPC (1,2-dihexadecanoyl-sn-glycero-3-phosphocholine) Langmuir−Blodgett (LB) films were deposited on hydrophilic mica and hydrophobic highly ordered pyrolitic graphite (HOPG), and subsequently characterized by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). AFM was used to determine the topography and to monitor the stability of the deposited films in air and under water at varying experimental parameters. Angle-resolved XPS was used to measure the mean thickness and the orientation of the deposit. Monolayer transfer pressure was determined at 40 mN/m with molecular area at 0.42 ± 0.02 nm2 for DPPE and 0.55 ± 0.02 nm2 for DPPC. Nanometric resolution was achieved on DPPE crystal and LB films and allowed the determination of the corresponding lattice constants a = 0.64 ± 0.03 nm, b = 0.91 ± 0.07 nm, and c = 5.6 ± 0.2 nm and a = 0.68 ± 0.02 nm, b = 0.93 ± 0.05 nm, and c = 5.6 ± 0.2 nm, respectively. The DPPE monolayer on mica was measured to be 2.7 ± 0.2 nm thick and the surface was hydrophobic. The reorganization of DPPE bilayer when going from the water to the air was directly observed to form monolayer and trilayer domains. On HOPG, the outermost layer of DPPE was partly hydrophilic and partly hydrophobic. Under the same conditions of deposition, DPPC formed a mixed structure of flat domains and vesicles. In water, monolayer aliphatic tail ending is less compact and presents a higher friction coefficient than polar heads as measured by lateral force AFM.
Sodium butyrate enhances fetal globin gene expression in erythroid progenitors of patients with Hb SS and beta thalassemia (1989)

Increasing the expression of the gamma globin genes is considered a useful therapeutic approach to the beta globin diseases. Because butyrate and alpha-amino-n-butyric acid (ABA) augment gamma globin expression in normal neonatal and adult erythroid progenitors, we investigated the effects of sodium butyrate and ABA on erythroid progenitors of patients with beta thalassemia and sickle cell anemia who might benefit from such an effect. Both substances increased fetal hemoglobin (Hb F) expression in Bfu-e from 7% to 30% above levels found in control cultures from the same subjects with sickle cell anemia. The fraction of cultured erythroblasts producing Hb F increased more than 20% with sodium butyrate treatment in 70% of cultures. In most cultures, this produced greater than 20% total Hb F and greater than 70% F cells, levels which have been considered beneficial in ameliorating clinical symptoms. Alpha: non-alpha (alpha-non-alpha) imbalance was decreased by 36% in erythroid progenitors of patients with beta thalassemia cultured in the presence of butyrate compared with control cultures from the same subjects. These data suggest that sodium butyrate may have therapeutic potential for increasing gamma globin expression in the beta globin diseases.
Role of Fluorescence Line-Narrowing Spectroscopy and Related Luminescence-Based Techniques in the Elucidation of Mechanisms of Tumor Initiation by Polycyclic Aromatic Hydrocarbons and Estrogens (2004)

Formation of DNA adducts by various carcinogens represents the first critical event in the mechanism of tumor initiation. The carcinogenic polycyclic aromatic hydrocarbons (PAHs) are biologically activated by two major mechanisms: one-electron oxidation to produce radical cations and monooxygenation to form bay-region diol epoxides. The PAH−DNA adducts formed by these mechanisms are stable adducts that remain in DNA unless removed by repair and depurinating adducts that are lost from DNA by cleavage of the glycosyl bond. Identification of PAH−DNA adducts has relied heavily on low-temperature, laser-based fluorescence spectroscopy under non-line-narrowing (NLN) and line-narrowing (FLN) conditions. These spectroscopies can be used for chemical identification, conformational analysis, and/or probing the microenvironment of DNA (or protein) adducts. Small and co-workers have pioneered the use of FLN spectroscopy in this research. For example, the structures of the depurinating adducts formed by the PAHs benzo[a]pyrene, 7,12-dimethylbenz[a]anthracene, and dibenzo[a,l]pyrene have been elucidated. Understanding of the mechanism of tumor initiation by PAHs has relied on identifying and quantifying the DNA adducts formed. The insights gained from the study of PAH−DNA adducts enabled us to discover the estrogen metabolites that form depurinating DNA adducts and can be potential endogenous initiators of human cancer. Small and co-workers have also studied the estrogen−DNA adducts and estrogen−thioether conjugates by using FLNS and related luminescence-based techniques and have demonstrated that the level of the 4-hydroxyestrone-1-N3-adenine depurinating adduct in breast tissue from a woman with breast carcinoma was significantly higher than that in breast tissue from women without breast cancer. The fluorescence- and phosphorescence-based techniques they are developing will be applied to analyzing estrogen adducts and conjugates as biomarkers of susceptibility to breast and other types of human cancer.
Hemophilia B Gene Therapy with a High-Specific-Activity Factor IX Variant (2017)

We found sustained therapeutic expression of factor IX coagulant activity after gene transfer in 10 participants with hemophilia who received the same vector dose. Transgene-derived factor IX coagulant activity enabled the termination of baseline prophylaxis and the near elimination of bleeding and factor use. (Funded by Spark Therapeutics and Pfizer; ClinicalTrials.gov number, NCT02484092 .).
Proteomic identification of biomarkers of traumatic brain injury (2005)

Traumatic brain injury (TBI) is a major national health problem without a US Food and Drug Administration-approved therapy. This review summarizes the importance of discovering relevant TBI protein biomarkers and presents logical rationale that neuroproteomic technologies are uniquely suited for the discovery of otherwise unnoticed TBI biomarkers. It highlights that one must make careful decisions when choosing which paradigm (human vs. animal models) and which biologic samples to use for such proteomic studies. It further outlines some of the desirable attributes of an ideal TBI biomarker and discusses how biomarkers discovered proteomically are complementary to those identified by traditional approaches. Lastly, the most important sequela of any proteomically identified TBI biomarker is validation in preclinical or clinical samples.
Control of Raman Lasing in the Nonimpulsive Regime (2004)

We explore coherent control of stimulated Raman scattering in the nonimpulsive regime. Optical pulse shaping of the coherent pump field leads to control over the stimulated Raman output. A model of the control mechanism is investigated.
Identification of Promiscuous Small Molecule Activators in High-Throughput Enzyme Activation Screens (2008)

It is recognized that high-throughput enzyme inhibition screens often return nonspecific inhibitors as "hits". Recently, high-throughput screens for enzyme activators have led to the identification of several compounds with novel and potent biological activity. Here, we show that enzyme activation screens can also uncover compounds that activate multiple enzymes in a nonspecific fashion. Described herein are the general structural features of such compounds and methods to differentiate between specific and general enzyme activation.
Angiogenin Single-Chain Immunofusions:  Influence of Peptide Linkers and Spacers between Fusion Protein Domains (1996)

The gene for human angiogenin (Ang), a member of the ribonuclease superfamily, was fused to a gene encoding a single-chain antibody (sFv) against the human transferrin receptor. Three Ang single-chain immunofusion proteins (AngsFvs) were constructed with variations in the type of linker connecting the VL and VH chain [EGKSSGSGSESKEF, L1 or (GGGGS)3, L2] as well as with or without a spacer (FB) connecting the Ang and sFv (AngFBsFvL1 or L2; AngsFv(L2)]. Although the nature of the linker did not affect the enzymatic activity of the FB-containing fusion proteins, the fusion protein containing the L2 linker was 2.3-fold more effective than the L1 linker in competing with the labeled monoclonal IgG1 antibody for binding to the transferrin receptor. The fusion protein containing the L2 linker without the FB spacer exhibited a 13-fold decrease in binding to the transferrin receptor as well as a decrease in its capacity to degrade tRNA and to inhibit translation in the rabbit reticulocyte lysate compared to its counterpart containing the FB spacer. Binding of placental ribonuclease inhibitor (PRI) to Ang also was affected by the nature of the linker and by the presence or absence of a spacer. PRI bound to Ang and AngFBsFv(L2) and inhibited their ribonuclease activity. A 3-fold greater concentration of PRI, however, did not affect the activity of AngFBsFv(L1) or AngsFv(L2), suggesting that the conformation of these fusion proteins was altered. Binding of monoclonal and polyclonal anti-Ang antibodies to AngsFvs was also used to investigate conformational alterations of the fusion proteins. AngFBsFv(L2) was the least altered while AngFBsFv(L1) exhibited the greatest change in structure. Yet maximal concentrations of all AngsFvs elicited angiogenesis in the chick chorioallantoic membrane assay, demonstrating that Ang in all three fusion proteins remained functionally active. Consistent with all the activities, the fusion protein containing the FB spacer and L2 linker was the most cytotoxic to three different human tumor cell lines. The fusion protein lacking the FB spacer exhibited the least cytotoxicity. These data demonstrate that the linker connecting the VH-VL chains can affect the binding and cellular cytotoxicity of Ang immunofusions and that placement of a spacer between the antibody binding domains and Ang is necessary for optimal activity. Thus, a new class of targeted therapeutic agents containing Ang as the toxic moiety can be designed that potentially will be less immunogenic and less toxic than immunotoxins available currently.
Assembly of Ultrathin Polymer Multilayer Films by Click Chemistry (2006)

Layer-by-layer (LbL) assembly is a versatile and robust technique for fabricating tailored thin films of diverse composition. Herein we report a new method of covalent coupling, click chemistry, to facilitate the LbL assembly of thin films. Linear film growth was observed using both UV-vis and FTIR spectroscopy, and film thicknesses were determined by ellipsometry and atomic force microscopy. The assembled films are shown to be stable in a wide pH range. This technique offers the potential to enable the synthesis of new types of stable and responsive LbL films from a variety of polymers.