gebhart/patrepeval huggingface dataset:
Membrane fusion activity, oligomerization, and assembly of the rabies virus glycoprotein (1991)

The spike glycoprotein (G protein) of rabies virus (CVS strain) expressed in HeLa cells from cloned cDNA mediated membrane fusion after exposure to pHs of 6.1 or below. Chemical crosslinking showed that the rabies G protein, like the vesicular stomatitis virus (VSV) G protein, could be crosslinked to dimers and trimers, indicating that rabies G protein is a trimer. However, unlike the VSV G protein, rabies G protein trimers were not stable to sedimentation in sucrose gradients, even at a mildly acidic pH which stabilizes the VSV G protein trimers. In addition, we report that the expressed rabies virus G protein was functional because it could assemble into VSV particles (tsO45) lacking VSV G protein and rescue infectivity. These VSV (rabies) pseudotypes were neutralized only by an antibody to the rabies G protein. We also examined the properties of a hybrid protein containing the extracellular domain of the rabies virus glycoprotein and the transmembrane and cytoplasmic domains of the VSV G protein. This protein was transported to the cell surface and could be crosslinked to form dimers and trimers, but had little or no detectable membrane fusion activity. The lack of fusion activity was paradoxical because the hybrid protein could rescue VSV infectivity, although the titers were lower than those obtained with the wild-type rabies G protein.
Optimal decentralized protocol for electric vehicle charging (2011)

Motivated by the power-grid-side challenges in the integration of electric vehicles, we propose a decentralized protocol for negotiating day-ahead charging schedules for electric vehicles. The overall goal is to shift the load due to electric vehicles to fill the overnight electricity demand valley. In each iteration of the proposed protocol, electric vehicles choose their own charging profiles for the following day according to the price profile broadcast by the utility, and the utility updates the price profile to guide their behavior. This protocol is guaranteed to converge, irrespective of the specifications (e.g., maximum charging rate and deadline) of electric vehicles. At convergence, the l <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> norm of the aggregated demand is minimized, and the aggregated demand profile is as “flat” as it can possibly be. The proposed protocol needs no coordination among the electric vehicles, hence requires low communication and computation capability. Simulation results demonstrate convergence to optimal collections of charging profiles within few iterations.
Acoustics (2004)

Abstract State‐of‐the‐art computational methods for linear acoustics are reviewed. The equations of linear acoustics are summarized and then transformed to the frequency domain for time‐harmonic waves governed by the Helmholtz equation. Two major current challenges in the field are specifically addressed: numerical dispersion errors that arise in the approximation of short unresolved waves, polluting resolved scales and requiring a large computational effort, and the effective treatment of unbounded domains by domain‐based methods. A discussion of the indefinite sesquilinear forms in the corresponding weak form are summarized. A priori error estimates, including both dispersion (phase error) and global pollution effects for moderate to large wave numbers in finite element methods, are discussed. Stabilized and other wave‐based discretization methods are reviewed. Domain‐based methods for modeling exterior domains are described including Dirichlet‐to‐Neumann (DtN) methods, absorbing boundary conditions, infinite elements, and the perfectly matched layer (PML). Efficient equation‐solving methods for the resulting complex‐symmetric (non‐Hermitian) matrix systems are discussed including parallel iterative methods and domain decomposition methods including the FETI‐H method. Numerical methods for direct solution of the acoustic wave equation in the time domain are reviewed.
Single‐Carbon‐Atomic‐Resolution Detection of Odorant Molecules using a Human Olfactory Receptor‐based Bioelectronic Nose (2008)

Single-carbon-atomic-resolution detection of odorant molecules has been demonstrated using a human olfactory receptor-based bioelectric nose. Furthermore, since the human olfactory receptor is a G-protein-coupled receptor (GPCR), these sensor systems may be a new powerful platform for the development of new drugs and fragrances.
Abstract 3640: Novel humanized anti-Sialyl-Tn, anti-CD3 bispecific antibodies demonstrate tumor and T-cell specificity for immune activation at the tumor site (2017)

Abstract Tumor-associated carbohydrate antigens (TACAs) historically have been challenging targets for antibody therapeutics. Sialyl-Tn (STn) is a cancer specific antigen that is expressed on the surface of carcinomas including ovarian, colon, prostate, and pancreatic tumors but is rarely present in normal tissue. STn expression has been linked to innate immune suppression, a chemoresistant phenotype, metastasis, and poor prognosis. Previous attempts to target this antigen in the clinic with synthetic glycan vaccines proved safe but lacked efficacy. We have developed humanized bispecific antibodies targeting STn and CD3 for T-cell recruitment and activation at the tumor site. These bispecific antibodies were selected for optimal tumor targeting using our glycan microarray that enriches for candidates whose binding is protein-independent and glycan specific. STn-selective binding was demonstrated. Current lead candidates exhibited low nanomolar EC50 binding in flow cytometric assays against both STn expressing tumor cells and T cells. Quantification of T-cell activation and T-cell induced tumor killing in vitro provides a basis for the further clinical development of these bispecific antibody candidates. Citation Format: David A. Eavarone, Jillian Prendergast, Patricia E. Rao, Jenna Stein, Jeff Behrens, Daniel T. Dransfield. Novel humanized anti-Sialyl-Tn, anti-CD3 bispecific antibodies demonstrate tumor and T-cell specificity for immune activation at the tumor site [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3640. doi:10.1158/1538-7445.AM2017-3640
DAMPs, PAMPs and alarmins: all we need to know about danger (2006)

Multicellular animals detect pathogens via a set of receptors that recognize pathogen-associated molecular patterns (PAMPs). However, pathogens are not the only causative agents of tissue and cell damage: trauma is another one. Evidence is accumulating that trauma and its associated tissue damage are recognized at the cell level via receptor-mediated detection of intracellular proteins released by the dead cells. The term "alarmin" is proposed to categorize such endogenous molecules that signal tissue and cell damage. Intriguingly, effector cells of innate and adaptive immunity can secrete alarmins via nonclassical pathways and often do so when they are activated by PAMPs or other alarmins. Endogenous alarmins and exogenous PAMPs therefore convey a similar message and elicit similar responses; they can be considered subgroups of a larger set, the damage-associated molecular patterns (DAMPs).
Use of Florbetapir-PET for Imaging β-Amyloid Pathology (2011)

Florbetapir-PET imaging was correlated with the presence and density of β-amyloid. These data provide evidence that a molecular imaging procedure can identify β-amyloid pathology in the brains of individuals during life. Additional studies are required to understand the appropriate use of florbetapir-PET imaging in the clinical diagnosis of Alzheimer disease and for the prediction of progression to dementia.
A 13.56MHz RFID device and software for mobile systems (2005)

We report a new electronic device and software with the ability to write data to and read data from contact-less mobile systems adapting electromagnetic inductive coupling. Establishing electromagnetic-field simulation based on the finite element method (FEM) and using a new magnetic material, we have developed a small, thin radio frequency identification (RFID) device on metallic housing. Furthermore, device-driver and network-library software have been developed for use in cashless mobile systems as electronic money.
4-Hydroxynonenal Mimics Ozone-Induced Modulation of Macrophage Function Ex Vivo (1996)

Ozone is a ubiquitous pollutant that can cause acute pulmonary inflammation, cellular injury and may contribute to the development or exacerbation of chronic lung diseases. Despite much research, the effects of ozone on humans and potential cellular mechanisms of injury are still uncertain. However, ozone has been reported to increase the formation of aldehydes that could react with cellular proteins. Therefore, the purpose of these studies was to determine whether 4-hydroxynonenal (HNE), a previously unidentified aldehyde product of ozone exposure, is formed in human subjects exposed to ozone, and whether the response of human alveolar macrophages (AM) following a 1-h exposure to 0.25 ppm ozone with moderate exercise could be mimicked by in vitro incubation of AM with HNE. Western analysis demonstrated increased HNE protein adducts in airway fluid and alveolar macrophages after ozone exposure. AM were examined for endotoxin (lipopolysaccharide [LPS])-stimulated interleukin-1 beta (IL-1 beta) release and expression of heat shock protein 72 (HSP72). Immediately after ozone exposure there was no change in HSP72, but a 5-fold increase occurred 4 h after exposure. By 18 h after exposure, HSP72 levels decreased to below comparable air-exposed levels. Immediately after ozone exposure there was no effect on IL-1 beta release stimulated by LPS. However, IL-1 beta release stimulated by LPS was significantly inhibited 4 h after ozone exposure. By 18 h after ozone exposure, IL-1 beta release stimulated by LPS returned to normal. Incubation of human AM in vitro with HNE induced HSP72 and blocked LPS-stimulated IL-1 beta release possibly by inhibiting interleukin converting enzyme. Consequently, the in vitro results and demonstration of HNE protein adducts following ozone exposure are consistent with HNE being involved in this process in vivo and suggest that the cellular toxic effects of ozone could be a result of thiol reactive aldehydes produced by ozone.
PHYSIOLOGICAL EFFECTS OF HIGH AND LOW VOLTAGE PULSE COMBINATIONS FOR GENE ELECTROTRANSFER IN MUSCLE (2008)

Gene transfer by electroporation is gaining momentum as high level long term expression of transgenes can be obtained. Several different pulse regimens are efficient, yet little information is available on the physiological muscular response to gene electrotransfer. This paper provides a comprehensive evaluation of the physiological and molecular effects on host tissue after DNA electrotransfer. We have tested several pulse regimens with special emphasis on the pulse combination of a short (100 micros) high volt-age (HV) pulse followed by a long low voltage (LV) used for DNA electrotransfer, comparing it with 8 HV pulses designed to ensure extensive permeabilization of the muscle membrane. Using both mouse and rat skeletal muscle tissue, we investigated cell permeabilization by the 51Cr-EDTA assay, LDH release, Na+ and Ca2+ influx, K+ efflux, ATP release and water content, as well as muscle function both in vivo and ex vivo, Hsp-70 induction and histology. In all these assays, the HV+LV pulse combination gave rise to minimal disturbance of cell function, in all cases significantly different from results when using 8 HV pulses. The evaluated parameters were normalized after 1 week. The addition of DNA caused significantly more transmembrane exchange, and this may be due to entrance of the DNA through the membrane. In conclusion, this study comprehensively documents the immediate effects of DNA electro-transfer and shows that only slight cell disturbances occur with the HV+LV pulses used for gene transfer. This is highly important, as minimal perturbation of cell physiology is essential for efficient transgene expres-sion.
Dialyzable transfer factor in experimental Chagas' disease: in vitro studies. (1986)

The dialyzable transfer factor (TF) was prepared from spleen and lymph node cells of either normal (TFn) or infected (TFi) mice with Trypanosoma cruzi. The ability of TFn and TFi in transferring cellular immunity to T. cruzi antigens was assessed by the macrophage migration inhibition assay and lymphocyte transformation test. The results obtained with these two immunological assays indicated that only TFi is able to transfer cellular immune responses. This phenomenon was antigen specific. The content of free amino acids in TFi preparation was higher than in TFn. However, our data indicated that the stimulation of lymphocyte transformation is not due to the increase in glycine and serine. This activity of TFi required the addition of T. cruzi antigens. Our findings support the hypothesis that TFi is derived from immune RNA.
.beta.-Adrenoceptor blocking activity of halogenated thienylethanolamine derivatives (1977)

\nFrom the archives of Untitled, Radio, this episode explores our relationship with travel and what it means to experience an “other.” This episode features artists, musicians, writers including Meriem Bennani, Marina Reyes Franco, Hector Arce Espasas, Sara Ludy, Sadria Baniasadi, Prem Krishnamurthy and Maayann Strauss, Mera and Don Rubell, Andy Rappaport, William S Smith, as well as an original score by Celia Hollander.\n\n
Cytokines, Chemokines, and Colony-Stimulating Factors in Human Milk: The 1997 Update (1998)

Epidemiologic studies conducted over the past 30 years to investigate the protective functions of human milk strongly support the notion that breast-feeding prevents infantile infections, particularly those affecting the gastrointestinal and respiratory tracts. However, more recent clinical and experimental observations also suggest that human milk not only provides passive protection, but also can directly modulate the immunological development of the recipient infant. The study of this remarkable defense system in human milk has been difficult due to its biochemical complexity, the small concentration of certain bioactive components, the compartmentalization of some of these agents, the dynamic quantitative and qualitative changes of milk during lactation, and the lack of specific reagents to quantify these agents. Nevertheless, a host of bioactive substances including hormones, growth factors, and immunological factors such as cytokines have been identified in human milk. Cytokines are pluripotent polypeptides that act in autocrine/paracrine fashions by binding to specific cellular receptors. They operate in networks and orchestrate the development and functions of the immune system. Several different cytokines and chemokines have been discovered in human milk over the past years, and the list is growing very rapidly. This article will review the current knowledge about the increasingly complex network of chemoattractants, activators, and anti-inflammatory cytokines present in human milk and their potential role in compensating for the developmental delay of the neonate immune system.
Synthesis of a Metallopeptide−PNA Conjugate and Its Oxidative Cross-Linking to a DNA Target (2004)

A nickel(II)-PNA bioconjugate was prepared by formation of a salicylaldimine complex with the amino terminus of a peptide-PNA hybrid with the sequence Arg-His-Gly-[TACCTAGCAT]PNA-Arg-CONH2. Hybridization to complementary oligodeoxynucleotides was demonstrated, and covalent adduct formation was observed upon addition of KHSO5 as oxidant. In the absence of PNA, the reactivity of the phenolic radical generated as an intermediate was found to be G >> T >> C, A; by inclusion of the PNA delivery agent, cross-links between the two oligomers could be observed with T and C bases in the vicinity of the nickel complex, although G was still the most reactive site. The metal complex could be removed by treatment with EDTA following which the Schiff base linkage was readily hydrolyzed. The final result in this case is a salicylaldehyde moiety appended at the target site in DNA.
Rabbit liver growth hormone receptor and serum binding protein. Purification, characterization, and sequence. (1988)

A putative growth hormone receptor from detergent-solubilized rabbit liver membranes and the growth hormone binding protein from rabbit serum have been purified 59,000- and 400,000-fold, respectively, primarily by affinity chromatography. Both purified proteins exhibit high affinity binding for human growth hormone; K alpha = 9-30 x 10(9) M-1 for the liver receptor and K alpha = 6 x 10(9) M-1 for the binding protein. The apparent molecular weight of the liver receptor is 130,000 by reduced sodium dodecyl sulfate gel electrophoresis, while that of the binding protein is 51,000. Both contain N-linked carbohydrate. The amino-terminal sequences of the liver growth hormone receptor and the serum binding protein were found to be the same, indicating that the binding protein corresponds to the extracellular domain of the liver receptor. Ubiquitin was found covalently linked to the liver receptor but not to the serum binding protein. The amino acid sequences of several peptides from the liver receptor were also determined after tryptic and V8 protease digestion.
SirR, a Novel Iron-Dependent Repressor inStaphylococcus epidermidis (1998)

In Staphylococcus epidermidis and Staphylococcus aureus, a number of cell wall- and cytoplasmic membrane-associated lipoproteins are induced in response to iron starvation. To gain insights into the molecular basis of iron-dependent gene regulation in the staphylococci, we sequenced the DNA upstream of the 3-kb S. epidermidis sitABC operon, which Northern blot analysis indicates is transcriptionally regulated by the growth medium iron content. We identified two DNA sequences which are homologous to elements of the Corynebacterium diphtheriae DtxR regulon, which controls, in response to iron stress, for example, production of diphtheria toxin, siderophore, and a heme oxygenase. Upstream of thesitABC operon and divergently transcribed lies a 645-bp open reading frame (ORF), which codes for a polypeptide of approximately 25 kDa with homology to the DtxR family of metal-dependent repressor proteins. This ORF has been designated SirR (staphylococcal iron regulator repressor). Within thesitABC promoter/operator region, we also located a region of dyad symmetry overlapping the transcriptional start ofsitABC which shows high homology to the DtxR operator consensus sequence, suggesting that this region, termed the Sir box, is the SirR-binding site. The SirR protein was overexpressed, purified, and used in DNA mobility shift assays; SirR retarded the migration of a synthetic oligonucleotide based on the Sir box in a metal (Fe2+ or Mn2+)-dependent manner, providing confirmatory evidence that this motif is the SirR-binding site. Furthermore, Southern blot analysis of staphylococcal chromosomal DNA with the synthetic Sir box as a probe confirmed that there are at least five Sir boxes in the S. epidermidis genome and at least three in the genome of S. aureus, suggesting that SirR controls the expression of multiple target genes. Using a monospecific polyclonal antibody raised against SirR to probe Western blots of whole-cell lysates of S. aureus, S. carnosus,S. epidermidis, S. hominis, S. cohnii, S. lugdunensis, and S. haemolyticus, we identified an approximately 25-kDa cross-reactive protein in each of the staphylococcal species examined. Taken together, these data suggest that SirR functions as a divalent metal cation-dependent transcriptional repressor which is widespread among the staphylococci.
Lossless Coding for Audio Discs (1996)

Strategies are presented that are being used to achieve efficient lossless compression or packing of PCM audio waveform data, allowing storage and transmission at greatly reduced data rates without any alteration of the signal. The disadvantages of simpler difference schemes and the benefits of more advanced schemes using IIR prediction with Huffman coding are explained and described, particularly with regard to the unique requirements of the future high-quality audio disc (HQAD) standard using high-density CD media.
Biomarkers for systemic lupus erythematosus: a review and perspective (2005)

There is a longstanding and recently rejuvenated enthusiasm for biomarkers that precisely and specifically reflect the pathophysiologic and clinical changes in systemic lupus erythematosus. Promising candidate biomarkers have been identified but must still be validated through rigorous, large-scale multicenter studies.
Stem cell factor induces phosphatidylinositol 3′-kinase–dependent Lyn/Tec/Dok-1 complex formation in hematopoietic cells (2000)

Stem cell factor (SCF) has an important role in the proliferation, differentiation, survival, and migration of hematopoietic cells. SCF exerts its effects by binding to cKit, a receptor with intrinsic tyrosine kinase activity. Activation of phosphatidylinositol 3'-kinase (PI3-K) by cKit was previously shown to contribute to many SCF-induced cellular responses. Therefore, PI3-K-dependent signaling pathways activated by SCF were investigated. The PI3-K-dependent activation and phosphorylation of the tyrosine kinase Tec and the adapter molecule p62Dok-1 are reported. The study shows that Tec and Dok-1 form a stable complex with Lyn and 2 unidentified phosphoproteins of 56 and 140 kd. Both the Tec homology and the SH2 domain of Tec were identified as being required for the interaction with Dok-1, whereas 2 domains in Dok-1 appeared to mediate the association with Tec. In addition, Tec and Lyn were shown to phosphorylate Dok-1, whereas phosphorylated Dok-1 was demonstrated to bind to the SH2 domains of several signaling molecules activated by SCF, including Abl, CrkL, SHIP, and PLCgamma-1, but not those of Vav and Shc. These findings suggest that p62Dok-1 may function as an important scaffold molecule in cKit-mediated signaling.
Percutaneous transjugular portosystemic shunt (1991)

<h3>Objective.</h3> —To determine the effectiveness of the Palmaz balloon expandable stent for the creation of a transjugular intrahepatic portosystemic shunt. The device is designed to achieve portal decompression in patients with variceal hemorrhage secondary to portal hypertension. <h3>Design.</h3> —Transjugular intrahepatic portosystemic shunting was performed in eight patients during a 9-month period. Mean follow-up was 5 months. <h3>Patients.</h3><h3>—</h3> All patients had cirrhosis with portal hypertension and varices. Bleeding occurred in seven patients from esophageal varices and in one patient from hemorrhoids. <h3>Main Outcome Measures.—</h3> Shunt patency and recurrent variceal hemorrhage. <h3>Results.</h3> —Shunts created from a transjugular approach between a hepatic and a portal vein (diameters of 8 to 12 mm) lowered the average portosystemic pressure gradient from 36 to 11 mm Hg. Mean postoperative hospital stay was 7.7 days. Complete variceal decompression after transjugular intrahepatic portosystemic shunt placement was identified endoscopically in all eight patients. The patient treated for hemorrhoids rebled and was treated successfully by transfemoral balloon expansion of the shunt diameter from 8 to 12 mm. All shunts were patent at 1 to 9 months (mean, 5 months) of follow-up. <h3>Conclusion.</h3> —Initial results suggest that transjugular intrahepatic portosystemic shunt is a safe and effective method of portal decompression for the treatment of variceal hemorrhage. (<i>JAMA</i>. 1991;266:390-393)