gebhart/patrepeval huggingface dataset:
Tau Trimers Are the Minimal Propagation Unit Spontaneously Internalized to Seed Intracellular Aggregation (2015)

Tau amyloid assemblies propagate aggregation from the outside to the inside of a cell, which may mediate progression of the tauopathies. The critical size of Tau assemblies, or "seeds," responsible for this activity is currently unknown, but this could be important for the design of effective therapies. We studied recombinant Tau repeat domain (RD) and Tau assemblies purified from Alzheimer disease (AD) brain composed largely of full-length Tau. Large RD fibrils were first sonicated to create a range of assembly sizes. We confirmed our ability to resolve stable assemblies ranging from n = 1 to >100 units of Tau using size exclusion chromatography, fluorescence correlation spectroscopy, cross-linking followed by Western blot, and mass spectrometry. All recombinant Tau assemblies bound heparan sulfate proteoglycans on the cell surface, which are required for Tau uptake and seeding, because they were equivalently sensitive to inhibition by heparin and chlorate. However, cells only internalized RD assemblies of n ≥ 3 units. We next analyzed Tau assemblies from AD or control brains. AD brains contained aggregated species, whereas normal brains had predominantly monomer, and no evidence of large assemblies. HEK293 cells and primary neurons spontaneously internalized Tau of n ≥ 3 units from AD brain in a heparin- and chlorate-sensitive manner. Only n ≥ 3-unit assemblies from AD brain spontaneously seeded intracellular Tau aggregation in HEK293 cells. These results indicate that a clear minimum size (n = 3) of Tau seed exists for spontaneous propagation of Tau aggregation from the outside to the inside of a cell, whereas many larger sizes of soluble aggregates trigger uptake and seeding.
Reliability of fluoride fiber module for optical amplifier use (1999)

We report reliability test results for a fluoride fiber module. We developed a sealed fluoride fiber module for practical optical fiber amplifier use. Trouble-free damp heat storage and low-temperature storage for 5000 h and trouble-free temperature cycling and temperature-humidity cycling tests revealed that our fluoride fiber module has long-term stability under practical environmental conditions.
Synthesis of Peptides and Proteins without Cysteine Residues by Native Chemical Ligation Combined with Desulfurization (2001)

The highly chemoselective reaction between unprotected peptides bearing an N-terminal Cys residue and a C-terminal thioester enables the total and semi-synthesis of complex polypeptides. Here we extend the utility of this native chemical ligation approach to non-cysteine containing peptides. Since alanine is a common amino acid in proteins, ligation at this residue would be of great utility. To achieve this goal, a specific alanine residue in the parent protein is replaced with cysteine to facilitate synthesis by native chemical ligation. Following ligation, selective desulfurization of the resulting unprotected polypeptide product with H(2)/metal reagents converts the cysteine residue to alanine. This approach, which provides a general method to prepare alanyl proteins from their cysteinyl forms, can be used to chemically synthesize a variety of polypeptides, as demonstrated by the total chemical syntheses of the cyclic antibiotic microcin J25, the 56-amino acid streptococcal protein G B1 domain, and a variant of the 110-amino acid ribonuclease, barnase.
Nitric Oxide Inhibition of Lipid Peroxidation:  Kinetics of Reaction with Lipid Peroxyl Radicals and Comparison with α-Tocopherol (1997)

The reaction between nitric oxide (*NO) and lipid peroxyl radicals (LOO*) has been proposed to account for the potent inhibitory properties of *NO toward lipid peroxidation processes; however, the mechanisms of this reaction, including kinetic parameters and nature of termination products, have not been defined. Here, the reaction between linoleate peroxyl radicals and *NO was examined using 2, 2'-azobis(2-amidinopropane) hydrochloride-dependent oxidation of linoleate. Addition of *NO (0.5-20 microM) to peroxidizing lipid led to cessation of oxygen uptake, which resumed at original rates when all *NO had been consumed. At high *NO concentrations (>3 microM), the time of inhibition (Tinh) of chain propagation became increasingly dependent on oxygen concentration, due to the competing reaction of oxygen with *NO. Kinetic analysis revealed that a simple radical-radical termination reaction (*NO:ROO* = 1:1) does not account for the inhibition of lipid oxidation by *NO, and at least two molecules of *NO are consumed per termination reaction. A mechanism is proposed whereby *NO first reacts with LOO* (k = 2 x 10(9) M-1 s-1) to form LOONO. Following decomposition of LOONO to LO* and *NO2, a second *NO is consumed via reaction with LO*, with the composite rate constant for this reaction being k = 7 x 10(4) M-1 s-1. At equal concentrations, greater inhibition of oxidation was observed with *NO than with alpha-tocopherol. Since *NO reacts with LOO* at an almost diffusion-limited rate, steady state concentrations of 30 nM *NO would effectively compete with endogenous alpha-tocopherol concentrations (about 20 microM) as a scavenger of LOO* in the lipid phase. This indicates that biological *NO concentrations (up to 2 microM) will significantly influence peroxidation reactions in vivo.
Loss compensation in dispersion compensation fiber modules by Raman amplification (2002)

Summary form only given. Dispersion-compensating fiber (DCF) devices relying on normal dispersion for the propagating mode are quite long (typically on the order of several kilometers) and therefore exhibit significant insertion loss. We propose and demonstrate Raman gain induced in the DCF as a simple and attractive method for obtaining lossless DCF modules. The Raman efficiency of the DCF is quite high because of the small mode-field diameter of the fiber, which leads to modest pump power requirements. A pump power of only 225 mW provides enough gain to offset the insertion loss of our 15.7-km DCF module with -1400 ps/nm of dispersion. We have also investigated the noise performance and verified penalty-free operation in a 9.953-Gbit/s transmission experiment.
Increased Expression of Catalase and Superoxide Dismutase 2 Reduces Cone Cell Death in Retinitis Pigmentosa (2009)

Oxidative and nitrosative damage are major contributors to cone cell death in retinitis pigmentosa (RP). In this study, we explored the effects of augmenting components of the endogenous antioxidant defense system in models of RP, rd1, and rd10 mice. Unexpectedly, overexpression of superoxide dismutase 1 (SOD1) in rd1 mice increased oxidative damage and accelerated cone cell death. With an elaborate mating scheme, genetically engineered rd10 mice with either inducible expression of SOD2, Catalase, or both in photoreceptor mitochondria were generated. Littermates with the same genetic background that did not have increased expression of SOD2 nor Catalase provided ideal controls. Coexpression of SOD2 and Catalase, but not either alone, significantly reduced oxidative damage in the retinas of postnatal day (P) 50 rd10 mice as measured by protein carbonyl content. Cone density was significantly greater in P50 rd10 mice with coexpression of SOD2 and Catalase together than rd10 mice that expressed SOD2 or Catalase alone, or expressed neither. Coexpression of SOD2 and Catalase in rd10 mice did not slow rod cell death. These data support the concept of bolstering the endogenous antioxidant defense system as a gene-based treatment strategy for RP, and also indicate that coexpression of multiple components may be needed.
The Cell Biology of Vertebrate Taste Receptors (1989)

New technologies in neurophysiology and ultrastructural research are bringing about rapid advances in our understanding of taste, particularly at the cellular level. The model of chemosensory processing in the taste bud presented here can now be explored in great detail. The synaptic organization of the taste bud indicates a potential for intriguing peripheral integrative mechanisms, including cross-talk between taste cells, summation of chemoreceptor responses by interneurons (basal cells) in the taste bud, and centrifugal control of taste buds via efferent input from the CNS. Figure 2 summarizes these findings. The existence of voltage-gated ionic channels on taste cells and their unequal distribution in apical and basolateral membrane suggests mechanisms for chemosensory transduction: A primary event in the transduction process for many taste stimuli is likely to be the closure of apical potassium channels, thus leading to a depolarizing receptor potential. The closure of these apical potassium channels is probably mediated via cyclic nucleotides or intracellular Ca2+.
Cytotoxic T lymphocyte antigen-4 (CTLA-4) regulates the size, reactivity, and function of a primed pool of CD4+T cells (2000)

We examined how cytotoxic T lymphocyte antigen-4 (CTLA-4) regulates heterogeneous CD4(+) T cell responses by using experimental autoimmune encephalomyelitis (EAE), a CD4(+) T cell-mediated disease that is subject to regulation by CTLA-4. Disease incidence and severity were used as measures of in vivo CD4(+) T cell responses. The frequency, cytokine production, and reactivity of primed T cells were determined from animals immunized with proteolipid protein (PLP)-139-151 (disease agonist), PLP-Q (disease antagonist), or both peptides, and treated with control or anti-CTLA-4 antibody to analyze the responding population. CTLA-4 blockade exacerbated disease in PLP-139-151-primed animals and overcame disease antagonism in coimmunized animals, but did not permit disease induction in PLP-Q-primed animals. Experimental autoimmune encephalomyelitis enhancement was associated with increased frequencies of cytokine-producing cells and increased ratios of IFN-gamma to IL-4 secretors responsive to PLP-139-151. Priming with PLP-Q elicited IL-4 and IL-2, but not IFN-gamma secretors cross-reactive with PLP-139-151. Strikingly, CTLA-4 blockade was found to decrease rather than increase the frequencies of cross-reactive IL-4 and IL-2 secretors. Thus, CTLA-4 engagement limits the size, but increases the breadth, of reactivity of a primed pool of CD4(+) T cells, consequently regulating its function.
Benefit of Glycoprotein IIb/IIIa Inhibition in Patients With Acute Coronary Syndromes and Troponin T–Positive Status (2001)

TnT predicts poor short-term outcomes in non-ST-segment elevation ACS. Treatment benefit with lamifiban is limited almost exclusively to TnT-positive patients, reducing 30-day adverse outcomes to a rate nearly identical to that of negative patients.
Lack of beneficial effects of L-arginine infusion in primary pulmonary hypertension. (1994)

The aim of this study was to assess the effects of L-arginine in primary pulmonary hypertension (PPH). Diagnostic cardiac catheterization was performed in 4 patients (pts) (1 man and 3 women, aged 18-47 years) with suspected PPH. In all of them diagnosis of PPH was confirmed; mean pulmonary artery pressure (PAP) ranged from 46 to 83 mmHg. Then 61/min oxygen was administered for 10 min through the oxygen mask (first oxygen test). After another 15 min, L-arginine was infused into an antecubital vein at a dose of 12.63g of L-arginine hydrochloride in 300 ml of 0.9% NaCl over 90 min. 15 min before the planned termination of the infusion the second oxygen test was performed in the same way as the first one. Hemodynamic data were collected by means of two catheters placed in the main pulmonary artery and in the aortic root. Cardiac output (CO) was estimated by the thermodilution technique. Blood samples were drawn from both catheters to estimate oxygen tension and cyclic GMP (cGMP) levels. In pts 1 and 2 differences between baseline values and following L-arginine did not exceed 9% for mean PAP (mPAP), total pulmonary resistance (TPR), mean aortic pressure (mAP), systemic resistance (SR), CO and HR. In patient 3 mAP and SR dropped by about 30%. In patient 4 after 15 min of the infusion mAP and SR fell by about 50%, whereupon we stopped L-arginine administration. Thus, for ethical reasons, we decided not to recruit new subjects for the study. In pts 1-3 aortic oxygen tension diminished by 10-15% on L-arginine.(ABSTRACT TRUNCATED AT 250 WORDS)
Activating and inhibitory nature of the murine paired immunoglobulin‐like receptor family (2001)

Clones for murine paired immunoglobulin-like receptors (PIR) were first isolated as those coding for type I transmembrane glycoproteins with six immunoglobulin-like domains homologous to human Fc alphaR, bovine Fc gamma2R, and other related receptors. However, they turned out to bind neither IgA nor other immunoglobulins in the case of the ectopic expression on COS-1 fibroblastic cells. PIR-A and B are expressed on a wide variety of cells in the murine immune system, such as in B cells, mast cells, macrophages, and dendritic cells, mostly in a pairwise fashion. PIR-A requires homodimeric Fc receptor common gamma chain, which harbors an immunoreceptor tyrosine-based activation motif, for its efficient cell surface expression and for the delivery of activation signaling. In contrast, PIR-B contains immunoreceptor tyrosine-based inhibitory motifs (ITIMs) in its cytoplasmic portion and inhibits receptor-mediated activation signaling in vitro upon engagement with other activating-type receptors such as the antigen receptor on B cells and the high affinity Fc receptor for IgE on mast cells. ITIMs of PIR-B on macrophages and B cells have been shown to be constitutively phosphorylated in their tyrosine residues. Although the ligand for PIR still remains unknown, the transgenics and the gene-targeted mice will provide us with valuable information on their physiological roles in the immune regulation.
Genomic biomarkers and cellular pathways of ischemic stroke by RNA gene expression profiling (2010)

Our study highlights the relevance of the innate immune system through toll-like receptor signaling as a mediator of response to ischemic stroke and supports the claim that gene expression profiling can be used to identify biomarkers of ischemic stroke. Further studies are needed to validate and refine these biomarkers for their diagnostic potential.
Dual Function of RGD-Modified VEGI-192 for Breast Cancer Treatment (2012)

Identification of endogenous angiogenesis inhibitors has led to development of an increasingly attractive strategy for cancer therapy and other angiogenesis-driven diseases. Vascular endothelial growth inhibitor (VEGI), a potent and relatively nontoxic endogenous angiogenesis inhibitor, has been intensively studied, and this work shed new light on developing promising anti-angiogenic strategies. It is well-documented that the RGD (Arg-Gly-Asp) motif exhibits high binding affinity to integrin α(v)β(3), which is abundantly expressed in cancer cells and specifically associated with angiogenesis on tumors. Here, we designed a fusion protein containing the special RGD-4C motif sequence and VEGI-192, aimed at offering more effective multiple targeting to tumor cells and tumor vasculature, and higher anti-angiogenic and antitumor efficacy. Functional tests demonstrated that the purified recombinant human RGD-VEGI-192 protein (rhRGD-VEGI-192) potently inhibited endothelial growth in vitro and suppressed neovascularization in chicken chorioallantoic membrane in vivo, to a higher degree as compared with rhVEGI-192 protein. More importantly, rhRGD-VEGI-192, but not rhVEGI-192 protein, could potentially target MDA-MB-435 breast tumor cells, significantly inhibiting growth of MDA-MB-435 cells in vitro, triggered apoptosis in MDA-MB-435 cells by activation of caspase-8 as well as caspase-3, which was mediated by activating the JNK signaling associated with upregulation of pro-apoptotic protein Puma, and consequently led to the observed significant antitumor effect in vivo against a human breast cancer xenograft. Our study indicated that the RGD-VEGI-192 fusion protein might represent a novel anti-angiogenic and antitumor strategy.
Non-invasive molecular imaging and reporter genes (2006)

Abstract Molecular-genetic imaging in living organisms has become a new field with the exceptional growth over the past 5 years. Modern imaging is based on three technologies: nuclear, magnetic resonance and optical imaging. Most current molecular-genetic imaging strategies are “indirect,” coupling a “reporter gene” with a complimentary “reporter probe.” The reporter transgene usually encodes for an enzyme, receptor or transporter that selectively interacts with a radiolabeled probe and results in accumulation of radioactivity in the transduced cell. In addition, reporter systems based on the expression of fluorescence or bioluminescence proteins are becoming more widely applied in small animal imaging. This review begins with a description of Positron Emission Tomography (PET)-based imaging genes and their complimentary radiolabeled probes that we think will be the first to enter clinical trials. Then we describe other imaging genes, mostly for optical imaging, which have been developed by investigators working with a variety of disease models in mice. Such optical reporters are unlikely to enter the clinic, at least not in the near-term. Reporter gene constructs can be driven by constitutive promoter elements and used to monitor gene therapy vectors and the efficacy of gene targeting and transduction, as well as to monitor adoptive cell-based therapies. Inducible promoters can be used as “sensors” to monitor endogenous cell processes, including specific intracellular molecular-genetic events and the activity of signaling pathways, by regulating the magnitude of reporter gene expression.
Amgen Halts Rilotumumab Development Due to Increased Death Signal (2014)

Amgen has halted clinical trials of rilotumumab in gastric cancer after a planned safety review showed an increase in the risk of death with the study drug.
Development of a Culture Medium (BECM-3) for Porcine Embryos: Effects of Bovine Serum Albumin and Fetal Bovine Serum on Embryo Development (1996)

Media are available that can deliver modest porcine embryonic development from a single-cell zygote to the blastocyst stage. However, few embryos develop to hatched blastocysts by Day 7 in vitro, indicating deficiencies in media that inhibit early embryonic development. A defined culture medium, Beltsville Embryo Culture Medium (BECM-3), was developed to support porcine zygote development to the blastocyst stage. When fetal bovine serum was added by late Day 5 (late morula/early blastocyst stage), 80% of total embryos cultured from Day 2 developed into hatched blastocysts by Day 8. There was also a significant increase in the mean cell number of blastocysts and hatched blastocysts when culture was performed in BECM-3-based media in the absence of BSA fraction V. These studies provide a chemically defined foundation for elucidating key developmental components of preimplantation pig embryos.
Osteoprotegerin ligand: A common link between osteoclastogenesis, lymph node formation and lymphocyte development (1999)

The TNF-family molecule osteoprotegerin ligand (OPGL; also known as TRANCE, RANKL or ODF) has been identified as the osteoclast differentiation factor and a regulator of T cell-dendritic cell interactions in the immune system. Surprisingly, the same molecule was identified as a crucial factor in early lymphocyte development and lymph node organogenesis. We will discuss the role of OPGL in bone remodelling and the immune system.
The isolation and characterisation of human atrial natriuretic factor produced as a fusion protein in Escherichia coli (1988)

Human atrial natriuretic factor [ANF(1–28)] has been isolated from a fusion protein produced in Escherichia coli. ANF(1–28) was linked to a naturally occurring E. coli protein, chloramphenicol acetyltransferase, via unique cleavage sequences susceptible to either human thrombin digestion, or the chemical action of 2‐(2‐nitrophenylsulphenyl)‐3‐methyl‐3′‐bromoindolenine (BNPS‐skatole). The linker sequences were Gly‐Val‐Arg‐Gly‐Pro‐Arg and Trp respectively. The liberated ANF was purified by reversed‐phase HPLC. Optimised cleavage conditions released 5–10% (by mass) of the maximal yield of ANF(1–28) from the fusion protein with the thrombin‐susceptible linker, whilst a 2–5% (by mass) yield was observed from the fusion protein with the tryptophan linker after BNPS‐skatole treatment. The purified cleavage products were biologically active and shown to comprise intact ANF(1–28). Fast‐atom‐bombardment mass spectrometry confirmed [MH] 4 of 3079 m/z , consistent with ANF(1–28).
Improvement of phosphorus availability by microbial phytase in broilers and pigs (1990)

Techniques have been developed to produce microbial phytase for addition to diets for simple-stomached animals, with the aim to improve phosphorus availability from phytate-P in plant sources. The activity of the crude microbial phytase showed pH optima at pH 5.5 and 2.5. The enzyme was able to degrade phytate in vitro in soya-bean meal, maize and a liquid compound feed for pigs. When microbial phytase was added to low-P diets for broilers the availability of P increased to over 60% and the amount of P in the droppings decreased by 50%. The growth rate and feed conversion ratio on the low-P diets containing microbial phytase were comparable to or even better than those obtained on control diets. Addition of microbial phytase to diets for growing pigs increased the apparent absorbability of P by 24%. The amount of P in the faeces was 35% lower.
Low Molecular Weight Heparin Improves Peritoneal Ultrafiltration and Blocks Complement and Coagulation (2005)

The acute inflammatory reaction to PD fluid involves the complement and coagulation cascades. Addition of LMWH to the PD fluid improves ultrafiltration, inhibits formation of thrombin, and potentially blocks C5a activity. The present results motivate further investigations of the IP cascade systems in PD.
Solubility of Haloether Anesthetics in Human and Animal Blood (2012)

Anesthetic partition coefficients differ significantly between humans and most animals for haloether anesthetics. Because of their similar λ B:G values, goats may be a better animal model for inhaled anesthetic pharmacokinetics in people.
Typing of hepatitis B virus genomes by a simplified polymerase chain reaction (1990)

The amplification of hepatitis B virus (HBV) DNA sequences in sera for molecular epidemiology of HBV is an important application of the polymerase chain reaction (PCR) with regard to HBV. To simplify the PCR for this purpose, the optimal concentrations of SDS and detergents for carrying out the proteinase K digestion and the amplification of DNA by Taq polymerase were evaluated. It was found that by using 1% deoxycholic acid as detergent for the proteinase K step and diluting the digest 10 times before carrying out the PCR, the phenol extraction of DNA became superfluous. The sensitivity of this procedure equalled that of PCR after phenol extraction on comparable amounts of serum. Four pairs of oligonucleotide primers were compared for amplification of HBV DNA sequences in 48 sera previously subtyped with respect to hepatitis B surface antigen (HBsAg), and in eight sera with different genotypes of HBV, representing the subtypes of HBsAg P1 to P8, defined at an international meeting [Couroucé-Pauty et al.: "HBs Antigen Subtypes." Basel: Karger, 1976]. Two primer pairs, selected from conserved regions in the X and S genes of HBV, gave a positive PCR with sera harbouring all the eight different strains of HBV, resulting in DNA fragments consistent with the sizes deduced from genome sequence data. Two other primer pairs were selected in order to discriminate genotypes with regard to differences between d/y and w/r strains.(ABSTRACT TRUNCATED AT 250 WORDS)