gebhart/patrepeval huggingface dataset:
Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase–Cas1 fusion protein (2016)

CRISPR systems mediate adaptive immunity in diverse prokaryotes. CRISPR-associated Cas1 and Cas2 proteins have been shown to enable adaptation to new threats in type I and II CRISPR systems by the acquisition of short segments of DNA (spacers) from invasive elements. In several type III CRISPR systems, Cas1 is naturally fused to a reverse transcriptase (RT). In the marine bacterium Marinomonas mediterranea (MMB-1), we showed that a RT-Cas1 fusion protein enables the acquisition of RNA spacers in vivo in a RT-dependent manner. In vitro, the MMB-1 RT-Cas1 and Cas2 proteins catalyze the ligation of RNA segments into the CRISPR array, which is followed by reverse transcription. These observations outline a host-mediated mechanism for reverse information flow from RNA to DNA.
Plasma amino acids imbalance in cirrhotic patients disturbs the tricarboxylic acid cycle of dendritic cell (2013)

An imbalance of plasma amino acids (AA) is observed cirrhotic patients. Here we report that the imbalance suppresses the maturation of dendritic cells (DCs) by reducing the intracellular ATP due to interference with the mitochondrial tricarboxylic acid (TCA) cycle. We used serum-free culture medium consistent with the average concentration of the plasma AA from a healthy volunteer (HCM) and that from patients with advanced cirrhosis (ACM). We compared the function of DCs and the metabolism of glucose-amino acids under each medium. The maturation and intracellular ATP of immature DCs were lower under ACM in spite of the enhancement of mitochondrial respiratory chain complex genes. Metabolomics revealed that the TCA cycle metabolite, fumarate and 2-oxoglutarate were increased in DCs generated under ACM. Consistent with in vitro, In CD1c(+) or CD14(+) cells from cirrhotic patients, the gene expression of 2-oxoglutarate-succinate-fumarate transition enzymes were significantly different from the cells of healthy controls.
Shiga-like toxin purges human lymphoma from bone marrow of severe combined immunodeficient mice (1996)

Shiga-like toxin-1 (SLT-1) is a bacterial toxin that kills cells by inhibiting protein synthesis. SLT-1 is composed of one cytotoxic A-subunit and five B-subunits that bind to CD77, a cell-surface glycolipid. In the human hematopoietic system, CD77 expression is restricted to a subset of activated B cells and derived cancers. Here we report that SLT-1 treatment of murine bone marrow ex vivo effectively cures severe combined immunodeficient mice of a human B-cell lymphoma xenograft while sparing normal hematopoietic precursor cells. Flow cytometry results using fluorescein isothiocyanate-labeled SLT-1 B-subunit show the high prevalence of expression of SLT-1 receptors (CD77) in human non-Hodgkin's lymphomas, especially follicular lymphomas. These results suggest the use of SLT-1 for the purging of human bone marrow before autologous bone marrow transplant in the case of CD77+ B-cell lymphomas as just one of many possible uses.
3D Time‐resolved contrast‐enhanced MR DSA: Advantages and tradeoffs (1998)

The 3D TRICKS method for contrast-enhanced, time-resolved MR DSA has been recently described. In this paper, computer simulations are used to investigate the relative frame rate, temporal window, artery-vein temporal separation, contrast-to-noise ratio, and spatial resolution of TRICKS and conventional scans for breath-hold and non-breath-hold applications. For non-breath-hold applications, TRICKS can be configured to provide increased CNR or spatial resolution at an increased frame rate, but with a longer temporal window when compared with a series of conventional scans in which the central portion of k-space is sampled at the same rate as for the TRICKS scans. For breath-hold applications, TRICKS typically provides three images with 75% of the conventional single acquisition spatial resolution and is more tolerant of variations in contrast curve shape within the field of view.
The 104-123 amino acid sequence of the beta-domain of von Hippel-Lindau gene product is sufficient to inhibit renal tumor growth and invasion. (2001)

The von Hippel-Lindau (VHL) tumor suppressor gene is mutated in patients with VHL disease and in the majority of patients with sporadic renal cell carcinomas (RCCs). RCCs are dependent on insulin-like growth factor-1 receptor-mediated signaling for tumor growth and invasion in vivo. Reintroduction of the VHL gene product (pVHL) can inhibit on insulin-like growth factor-I receptor-mediated signaling in RCC cells in vitro through interaction with protein kinase C delta and is mediated by a specific amino acid sequence (104-123) in the beta-domain of the pVHL. In the present study, the amino acid sequence (104-123) of the pVHL was conjugated to the protein transduction domain of HIV-TAT protein (TATFLAGVHL-peptide) to facilitate entry into cells, and we demonstrate that this amino acid region of VHL is sufficient to block proliferation and invasion of 786-O renal cancer cells in vitro. Furthermore, daily i.p. injections with the TATFLAGVHL peptide retarded and, in some cases, caused partial regression of renal tumors that were implanted in the dorsal flank of nude mice. Treatment with this peptide also inhibits the invasiveness of renal tumors. A 56% decrease in the proliferative index in tumors treated with the TATFLAGVHL-peptide versus control-peptide-treated mice was observed. Taken together, these results show the novel importance of a 20-amino acid sequence of the beta-domain of the VHL gene product capable of inhibiting tumor growth and invasion. These results lay the foundation for a unique approach toward treating RCCs using this small-molecular-weight peptide fused to the TAT-sequence, which may, in the future, be used alone or in conjunction with other therapies.
Hexascan: a new robotized scanning laser handpiece. (1990)

A variety of treatment techniques are used with both argon and tunable dye lasers. Each method has its unique advantages: however, all appear to share common limitations such as poor reproducibility, lack of homogeneous energy delivery, and inability to treat rapidly large cutaneous vascular disorders such as port-wine stains. These problems have recently been addressed with a new scanning device designed to automate or speed treatment and provide improved consistency in cosmetic results. Hexascan is a computerized, automated scanning device that allows for the rapid and easily reproducible treatment of large areas of skin using either the dye or argon laser. The scanning pattern is designed to promote uniform energy fluence and minimize unwanted thermal damage to nontarget tissue. Clinical trials using Hexascan with 577 nm and 585 nm wavelengths have shown good results with cutaneous vascular disorders. Utilizing blue-green argon wavelengths, markedly reduced scarring has been observed compared to traditional argon techniques. Use with 514 nm green only argon light has successfully removed a variety of benign brown pigmented cutaneous lesions.
Tissue Factor Expression on Macrophages in Coronary Plaques in Patients with Unstable Angina (1997)

Tissue factor is a membrane-bound glycoprotein that functions in the extrinsic pathway of blood coagulation by acting as a cofactor for factor VII, and the resulting complex leads to thrombin production in vivo. The purpose of the present study is to determine whether macrophages express tissue factor in human coronary atherosclerotic plaques. We examined directional coronary atherectomy specimens from 24 patients with unstable angina and 23 with stable exertional angina. In these specimens, macrophages were detected in 22 (92%) of 24 patients with unstable angina versus 12 (52%) of 23 with stable exertional angina (P = .003). The percentage of macrophage infiltration area was significantly larger in patients with unstable angina than in those with stable exertional angina (17 +/- 3% versus 6 +/- 2%, P = .008). The immunohistochemical double staining revealed the expression of tissue factor on macrophages in 18 (75%) of 24 patients with unstable angina versus 3 (13%) of 23 with stable exertional angina (P < .0001). Thrombus was identified in 20 (83%) of 24 patients with unstable angina versus 12 (52%) of 23 with stable exertional angina (P = .02). Fibrin deposition was mainly observed around macrophages expressing tissue factor in the patients with unstable angina. We have shown that tissue factor expression on macrophages was more frequent in coronary atherosclerotic plaques in patients with unstable angina. Tissue factor expressed on macrophages may play an important role in the thrombogenicity in coronary atherosclerotic plaques of these patients.
Selective lysis of NK-sensitive target cells by a soluble mediator released from murine spleen cells and human peripheral blood lymphocytes. (1981)

Abstract The mechanism of natural killer (NK) cell-mediated cytotoxicity was investigated by examining the susceptibility of NK target cells to lysis by soluble mediators. Evidence is presented that demonstrates that mediators released from a nonimmune effector population can selectively lyse NK target cells. A miniaturized Marbrook culture system was adapted to assay for soluble mediators. Effector cells cultured in the bottom well stimulated with PHA, Con A, or PHA-coated L929 fibroblasts released soluble mediators cytotoxic to NK target cells cultured in the top chamber. These mediators required an incubation period of 40 hr to cause significant target cell lysis as measured by trypan blue exclusion. Soluble mediators released from murine spleen cells lysed the NK-sensitive YAC-1 and RL♂1 targets but not the NK-insensitive P815, EL4, AKSL2, LA-6, or YAC and RL♂1 passaged in vivo. Human peripheral blood lymphocytes released mediators cytotoxic to the NK-sensitive K562 and Molt-4 target cells but not to the NK-insensitive Raji or IM-9 targets. The soluble mediator was released from cultures of spleen cells of various mouse strains, including the nude mouse, but not from thymocytes. Cellfree supernatants derived from spleen cell cultures could lyse NK targets when assayed in the Marbrook system. Studies with these supernatants containing the soluble mediator revealed that a) the m.w. of the mediator was greater than 12,000, b) it was stable at −20°C but was inactivated by heating at 100°C for 15 min, and c) its lytic activity was inhibited by the addition of α-methyl-d-mannoside, d-galactose, or N-acetyl-d-galactosamine at 25 to 50 mM. The relationship of the soluble mediator, conventional lymphotoxins, and the mechanism of lysis in direct NK CMC reactions is discussed.
Laboratory and clinical evaluation of new live influenza virus vaccines. Need for minimum requirements. (1978)

Recently, new methods for the selection of candidate live influenza vaccine viruses have become available. They are based on the characterization of the genetic material of these viruses and have been shown to correlate with attenuation for man. Adequately attenuated viruses have been obtained from various H3N2 strains using standard methods of attenuation for each strain. These vaccine strains met the criteria for live attenuated influenza virus vaccines: they were attenuated, non-transmissible and immunogenic. The use of modern methods of attenuation also allows rapid updating of live influenza virus vaccines. Laboratory methods used, the safety testing of candidate vaccines in animals and man will be discussed. There is an urgent need for standardization and for the establishment of minimum requirements and specifications.
Inhibition of BCR signaling using the Syk inhibitor TAK-659 prevents stroma-mediated signaling in chronic lymphocytic leukemia cells (2016)

Proliferation and survival of chronic lymphocytic leukemia (CLL) cells depend on microenvironmental signals coming from lymphoid organs. One of the key players involved in the crosstalk between CLL cells and the microenvironment is the B-cell receptor (BCR). Syk protein, a tyrosine kinase essential for BCR signaling, is therefore a rational candidate for targeted therapy in CLL. Against this background, we tested the efficacy of the highly specific Syk inhibitor TAK-659 in suppressing the favorable signaling derived from the microenvironment. To ex vivo mimic the microenvironment found in the proliferation centers, we co-cultured primary CLL cells with BM stromal cells (BMSC), CD40L and CpG ODN along with BCR stimulation. In this setting, TAK-659 inhibited the microenvironment-induced activation of Syk and downstream signaling molecules, without inhibiting the protein homologue ZAP-70 in T cells. Importantly, the pro-survival, proliferative, chemoresistant and activation effects promoted by the microenvironment were abrogated by TAK-659, which furthermore blocked CLL cell migration toward BMSC, CXCL12, and CXCL13. Combination of TAK-659 with other BCR inhibitors showed synergistic effect in inducing apoptosis, and the sequential addition of TAK-659 in ibrutinib-treated CLL cells induced significantly higher cytotoxicity. These findings provide a strong rationale for the clinical development of TAK-659 in CLL.
A Single M1 Residue in the β2 Subunit Alters Channel Gating of GABAA Receptor in Anesthetic Modulation and Direct Activation (2003)

General anesthetics allosterically modulate the activity of neuronal gamma-aminobutyric acid, type A (GABAA), receptors. Previous mutational studies from our laboratory and others have shown that the regions in transmembrane domain 1 (M1) and pre-M1 of alpha and beta subunits in GABA receptors are essential for positive modulation of GABA binding and function by the intravenous (IV) general anesthetics. Mutation of beta2Gly-219 to Phe corresponded in rho nearly eliminated the modulatory effect of IV anesthetics in alpha1/beta2/gamma2S combination. However, the general anesthetics retained the ability to directly open the channel of mutant G219F, and the apparent affinity for GABA was increased, and desensitization rate was reduced. In this study, we made additional single mutations such as 219 Ser, Cys, Ile, Asp, Arg, Tyr, and Trp. The larger side chains of the replacement residues produced the greatest reduction in enhancement of GABA currents by IV anesthetics at clinical concentrations (Trp > Tyr = Phe > Arg > Asp > Ile > Cys > Ser = wild type). Compared with a 2-3-fold response in wild type, pentobarbital and propofol enhanced less than 0.5-fold; etomidate and alphaxalone modulation was reduced from more than 4- to 1-fold in G219F, G219Y, and G219W. A linear correlation was observed between the volume of the residue at position 219 and the loss of modulation. An identical correlation was found for the effect of modulation on left-shift in the GABA EC50 value; furthermore, the same rank order of residues, related to size, was found for reduction in the maximal direct channel-gating by pentobarbital (1 mm) and etomidate (100 mum) and for increased apparent affinity for direct gating by the IV anesthetics.
Chemical Synthesis of Lymphotactin: A Glycosylated Chemokine with a C-Terminal Mucin-Like Domain (2001)

The synthesis of a 93-residue chemokine, lymphotactin, containing eight sites of O-linked glycosylation, was achieved using the technique of native chemical ligation. A single GalNAc residue was incorporated at each glycosylation site using standard Fmoc-chemistry to achieve the first total synthesis of a mucin-type glycoprotein. Using this approach quantities of homogeneous material were obtained for structural and functional analysis.
Formation and ethene substrate reactions of iridium(ii) porphyrin metal-centered dπ radicals (2001)

Monomeric iridium(II) porphyrin complexes of tetrakis(2,4,6-trialkylphenyl)porphyrin ligands that are generated by photolysis of the Ir–Me derivatives are found to have the dxy2 dz22 dxz,yz3 ground electron configuration which differs from the dxy2 dxz,yz4 dz21 configuration observed for the Co(II) and Rh(II) analogs; reactions of these Ir(II) species with ethene reflect both the metallo-radical reactivity and the varying steric demands for the series of porphyrin ligands.
Culture and Expansion of the Human Embryonic Stem Cell Line HS181, Evaluated in a Double-Color System (2004)

An approach of using RFP-transfected human foreskin fibroblasts (hFS-RFP) to support the growth of GFP expressing human embryonic stem cells (hES; HS181-GFP) is reported. The two-color system was applied to detect interactions between hFS and human embryonic stem cells (hES). After overnight culture, the hES cell colonies showed a behavior of "pushing away" the underlying feeder cells. This phenomenon occurred with both a low and high density of feeders. The density of the feeder cell layer, however, influenced the growth pattern of hES cell colonies. At a high feeder cell density, the hES colonies were more pointed and aligned with the direction of the fibroblasts, whereas less dense feeder layers allowed a more rounded and flat hES colony formation. Not surprisingly, a small fraction of mitotically inactivated feeder cells reattached after passage and remained viable in the cultures for up to four subsequent passages. The prospect of using the two-color system for detection of possible fusion events between hES cells and feeder cells was assessed by screening a large number of cell cultures for double RFP/EGFP expressing cells. The results indicate that fusion events are extremely rare (<10-6), or alternatively that after fusion the dual expression of both EGFP and RFP is not easily detected for other reasons. In summary, a two-color system allows analysis of colony formation and also helps to identify and follow the differentiation of cells.
Pulmonary Disease Associated with Pseudomonas aeruginosa in Cystic Fibrosis: Current Status of the Host-Bacterium Interaction (1985)

Journal Article Pulmonary Disease Associated with Pseudomonas aeruginosa in Cystic Fibrosis: Current Status of the Host-Bacterium Interaction Get access Gerald B. Pier Gerald B. Pier Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Infectious Diseases, Volume 151, Issue 4, April 1985, Pages 575–580, https://doi.org/10.1093/infdis/151.4.575 Published: 01 April 1985
Mesalazine release from coated tablets: effect of dietary fibre. (1991)

Delayed-release mesalazine formulations relay on pH-dependent coat dissolution to ensure delivery of 5-aminosalicylic acid (5-ASA) to the colon. As dietary fibre acidifies the colonic lumen we have studied the effect of fibre supplementation in 10 patients with quiescent colitis. Greater intake of dietary fibre was associated with a decrease in stool pH and an increase in stool frequency and faecal mass. However, the 24 h faecal and urinary excretion of 5-ASA and N-acetyl-5-ASA was unchanged. The percentage of total faecal ASA excreted as N-acetyl-5-ASA correlated with whole-gut transit time, suggesting that prolonged transit may be disadvantageous to patients with colitis as N-acetyl-5-ASA appears to be inactive.
Development of Multichannel Devices with an Array of Electrospray Tips for High-Throughput Mass Spectrometry (2000)

The basic principles of multichannel devices with an array of electrospray tips for high-throughput infusion electrospray ionization mass spectrometry (ESI-MS) have been developed. The prototype plastic devices were fabricated by casting from a solvent-resistant resin. The sample wells on the device were arranged in the format of the standard 96-microtiter well plate, with each sample well connected to an independent electrospray exit port via a microchannel with imbedded electrode. A second plastic plate with distribution microchannels was employed as a cover plate and pressure distributor. Nitrogen gas was used to pressurize individual wells for transport of sample into the electrospray exit port. The design of independent microchannels and electrospray exit ports allowed very high throughput and duty cycle, as well as elimination of any potential sample carryover. The device was placed on a computer-controlled translation stage for precise positioning of the electrospray exit ports in front of the mass spectrometer sampling orifice. High-throughput ESI-MS was demonstrated by analyzing 96 peptide samples in 480 s, corresponding to a potential throughput of 720 samples/h. As a model application, the device was used for the MS determination of inhibition constants of several inhibitors of HIV-1 protease.
Characterization of Tau in Cerebrospinal Fluid Using Mass Spectrometry (2008)

The neurodegenerative disorder Alzheimer's disease (AD) is the most common cause of dementia in the elderly. The presence of neurofibrillary tangles, consisting of hyperphosphorylated tau protein, is one of the major neuropathologic characteristics of the disease, making this protein an attractive biomarker for AD and a possible target for therapy. Here, we describe an optimized immunoprecipitation mass spectrometry method that enables, for the first time, detailed characterization of tau in human cerebrospinal fluid. The identities of putative tau fragments were confirmed using nanoflow liquid chromatography and tandem mass spectrometry. Nineteen tryptic fragments of tau were detected, of which 16 are found in all tau isoforms while 3 represented unique tau isoforms. These results pave the way for clinical CSF studies on the tauopathies.
Synthesis and biological evaluation of N4-substituted imidazo- and v-triazolo[4,5-d]pyridazine nucleosides (1993)

The chemical synthesis of certain N4-substituted imidazo[4,5-d]pyridazine and v-triazolo[4,5-d]-pyridazine nucleosides is described. In both series, the 4-chloro analogues, i.e., 4-chloro-1-(2,3,5-tri-O-acetyl-beta-D-ribofuranosyl)imidazo[4,5-d]pyr idazine (5a) and 4-chloro-1-(2,3,5-tri-O-acetyl-beta-D-ribofuranosyl)-v-triazolo[4,5- d]pyridazine (5b), were used as synthons to the target nucleosides. Nucleoside 5b was far more reactive toward nucleophilic displacements than 5a. Attempted deprotection of 5b was always accompanied with displacement of the 4-chloro substituent, whereas 5a was conveniently deacetylated without loss of the chloro group. Biological evaluation of the title nucleosides included antitumor studies and substrate/inhibition studies with certain purine-metabolizing enzymes. The corresponding adenosine analogues, i.e., 2-aza-3-deazaadenosine (6a) and 2,8-diaza-3-deazaadenosine (6b), were very slowly reacting substrates and weak inhibitors of bovine adenosine deaminase, whereas the inosine analogues were highly resistant to human purine nucleoside phosphorylase. The 4-benzylamino derivatives were weak inhibitors of adenosine transport into human erythrocytes. The inosine, adenosine, and selected N4-substituted analogues exhibited no in vitro toxicity toward murine L1210 leukemia and B16 melanoma cells.