gebhart/patrepeval huggingface dataset:
Human DNA-demethylating activity: A glycosylase associated with RNA and PCNA (2000)

We have partially purified and characterized the 5-methylcytosine removing activity (5-meC-DNA Glycosylase) from HeLa cells with 700-fold enrichment. This activity cleaves DNA specifically at fully methylated CpG sites. The mechanism of 5-meC removal is base excision from fully methylated CpG loci on DNA, producing abasic sites. Hemi-methylated DNA is not a substrate. A prominent 52 KDa protein is present in all partially purified fractions. This activity is tightly associated with other nuclear factors and proteins, which resulted in differential fractionation of this activity on ion exchange columns. One nuclear factor associated with this activity is identified as RNA. Another nuclear protein, proliferating cell nuclear antigen (PCNA) is also associated with this enzyme. Glycosylic removal of 5-meC from DNA by this activity could be involved in the regulation of transcription, replication, differentiation, and development through resultant hypomethylation of DNA.
A microfabricated inductively coupled plasma generator (2000)

The design, fabrication, and characterization of a surface micromachined plasma generator is described for the first time in this paper. The plasma is sustained without electrodes by inductively coupling a /spl sim/150-MHz current into a region of low-pressure gas, Both argon and air plasmas have been generated over a range of gas pressures from 0.1 to 10 torr (13.3-1333 Pa). Typically, the power used to sustain the plasma is 350 mW, although /spl sim/1.5 W is required to initiate the discharge. Network analysis of the plasma generator circuit shows that over 99% of the applied RF power can be absorbed by the device. Of this, /spl sim/50% is absorbed by the plasma and the remainder of the power is dissipated as ohmic heating. An argon ion current of up to 4.5 mA/cm/sup 2/ has been extracted from the plasma and the electron temperature is 52 000 K at 0.1 torr. This plasma source is intended for electronic excitation of gas samples so that the presence of impurities and toxins may be detected using optical emission spectroscopy.
Safety, Pharmacokinetics, and Antiviral Activity of AMD3100, a Selective CXCR4 Receptor Inhibitor, in HIV-1 Infection (2004)

AMD3100 is a CXCR4 receptor inhibitor with anti-HIV-1 activity in vitro. We tested the safety, pharmacokinetics, and antiviral effect of AMD3100 administered for 10 days by continuous intravenous infusion in an open-label dose escalation study from 2.5 to 160 microg/kg/h. Forty HIV-infected patients with an HIV RNA level >5000 copies/mL on stable antiretroviral (ARV) regimens or off therapy were enrolled. Syncytium-inducing (SI) phenotype in an MT-2 cell assay was required in higher dose cohorts. Most subjects were black (55%), male (98%), and off ARV therapy. HIV phenotype was SI (30%), non-SI (45%), or not tested (25%). One patient (5 microg/kg/h) had serious and possibly drug-related thrombocytopenia. Two patients (40 and 160 microg/kg/h) had unexpected, although not serious, premature ventricular contractions. Most patients in the 80- and 160-microg/kg/h cohorts had paresthesias. Steady-state blood concentration and area under the concentration-time curve were dose proportional across all dose levels; the median terminal elimination half-life was 8.6 hours (range: 8.1-11.1 hours). Leukocytosis was observed in all patients, with an estimated maximum effect of 3.4 times baseline (95% confidence interval: 2.9-3.9). Only 1 patient, the patient whose virus was confirmed to use purely CXCR4 and who also received the highest dose (160 microg/kg/h), had a significant 0.9-log10 copies/mL HIV RNA drop at day 11. Overall, however, the average change in viral load across all patients was +0.03 log10 HIV RNA. Given these results, AMD3100 is not being further developed for ARV therapy, but development continues for stem cell mobilization.
Cell Fractionation and Arrangement on Fibers, Beads, and Surfaces (1971)

A new method, fiber fractionation, has been used to isolate and separate cells. The cells are adsorbed to fibers covalently coupled to molecules such as antigens, antibodies, and lectins which can bind specifically to cell-surface components. The cells are then removed mechanically by plucking the taut fibers. Alternatively, competitive inhibitors of binding may be used to remove the cells at a lesser rate. Successful fractionations have been achieved by varying the degree of derivatization of the fibers by the lectin concanavalin A. Lymphoid cells have been separated by the use of different antigens coupled to the fibers. The method may also be used for specific fixation and manipulation of viable cell populations in culture. In addition to fibers, beads and surfaces have been specifically derivatized and used to achieve different geometrical arrangements of the cells.
Carcinoembryonic antigen family: expression in a mouse L-cell transfectant and characterization of a partial cDNA in bacteriophage lambda gt11. (1987)

Genomic DNA and mRNA from the adenocarcinoma cell line LoVo were used to generate L-cell transfectants and a bacteriophage lambda gt11 cDNA clone that express epitopes of carcinoembryonic antigen (CEA). Primary and secondary L-cell transfectants expressing CEA were selected with a fluorescence-activated cell sorter (FACS). These transfectants, including some clones that were selected for high-level CEA expression by multiple rounds of FACS sorting, express a surface protein of 150 kDa that reacts with all anti-CEA antibodies tested. In parallel, a cDNA library of LoVo poly(A)+ RNA was constructed in lambda gt11 and fusion proteins were screened with polyclonal antisera against CEA. One positive clone, lambda cLV7, was identified that hybridized specifically to transfectant DNA. The nucleic acid sequence of the cDNA insert (cLV7) contained two regions of extensive internal homology, with greater than 70% identity at the amino acid level. cLV7 hybridized to three mRNA species of LoVo cells and to a predominant mRNA of the CEA-expressing transfectants. Hybridization of cLV7 to restriction endonuclease-digested genomic DNA of colon carcinoma cells, normal human cells, and human-mouse somatic cell hybrids revealed the presence of multiple hybridizing bands, one of which was present in transfectant cells. These CEA-related sequences are not rearranged in tumors and, by somatic cell hybrid analysis, were mapped to human chromosome 19.
Pleiotropic Effect of the recA Gene of Escherichia coli: Uncoupling of Cell Division from Deoxyribonucleic Acid Replication (1971)

A defective recA gene, which is involved in recombination, is shown in this article to permit limited cell division, when deoxyribonucleic acid (DNA) synthesis is blocked. Thymidine starvation or nalidixic acid blocked DNA synthesis, and stopped cell division of a rec(+)thy(-) strain of Escherichia coli. However, with the same treatments, a recAthy(-) strain could continue to divide for at least 5 hr, and cell numbers increased 2.5- to 4-fold. After several hours of thymidine starvation, the culture contained very long cells (snakes) and small (normal-sized) cells. The short cells contained very little, if any, DNA. Cells of all ages divided in the absence of thymidine. Specific differences in membrane proteins were observed between thymidine-starved rec(+) and recA cells, as expected from previous experiments in which these proteins were associated with cell division and DNA synthesis. It is proposed that septum formation is controlled negatively by the recA(+) gene.
First-row transitional-metal oxalate resists for EUV (2018)

We have developed inorganic oxalate compounds [PPh3(CH2Ph)][M(2,2′-bipyridine)n(oxalate)(3-n)] (n=1, 2, 3; M = Co, Fe, Cr) capable of acting as negative-tone extreme ultraviolet (EUV) resists. Two important trends are observed: (1) sensitivity increases with the number of oxalate ligands; (2) Cobalt and iron complexes exhibit greater sensitivity than analogous chromium complexes. Lithographic studies of the most successful compound, [PPh3(CH2Ph)][Co(2,2′-bipyridine)(oxalate)2], show that it can consistently achieve 20 nm h/p lines at doses approaching 30 mJ/cm2. Infrared, paramagnetic nuclear magnetic resonance, and cyclic voltammetric studies of this compound show that the reaction products of the EUV photochemistry are Co(II)(2,2′-bipyridine)(oxalate) and [PPh3(CH2Ph)]2(oxalate) formed from the decomposition of one of the oxalate ligands into two equivalents each of carbon dioxide and electrons.
G alpha q family members couple parathyroid hormone (PTH)/PTH-related peptide and calcitonin receptors to phospholipase C in COS-7 cells. (1996)

The PTH/PTH-related peptide (PTHrP) receptor and the calcitonin receptor mediate the action of their physiological ligands by activating two different effectors, adenylyl cyclase and phospholipase C. Whereas regulation of adenylyl cyclase via both receptors is thought to involve the G protein G(s), it is not known whether activation of phospholipase C results from coupling of the receptors to G(q) family members or whether beta gamma-subunit released from receptor-activated G(s) lead to phospholipase C activation. To elucidate the mechanism of this type of dual signaling, we reconstituted the signal transduction of the PTH/PTHrP and the calcitonin receptor in COS-7 and HEK293 cells. In COS-7 cells expressing the receptor alone, addition of the respective ligands resulted in the accumulation of cAMP and inositol phosphates. When cells were cotransfected with the cDNAs of receptor and different alpha-subunits of the Gq family (G alpha q, G alpha 11, G alpha 14, G alpha 15, and G alpha 16, a severalfold increase in the ligand-dependent inositol phosphate production could be observed, indicating that the receptors functionally interacted with all alpha-subunits of the G alpha q family. Additionally, whereas PTH treatment of HEK293 cells coexpressing both the PTH/PTHrP receptor and G alpha q increased both second messengers, the same treatment in cells expressing the PTH/PTHrP receptor alone increased only cAMP. Under all conditions tested, activation of phospholipase C via the PTH/PTHrP and calcitonin receptor required higher ligand concentrations than receptor-mediated adenylyl cyclase activation. Our data strongly support the idea that dual signaling of the PTH/PTHrP and calcitonin receptors is due to the a activation of different G proteins belonging to the G(s) and G(q) families.
Acquired immunodeficiency syndrome-related Kaposi's sarcoma: clinical features, staging, and treatment. (2000)

The clinical course of acquired immunodeficiency syndrome (AIDS)-related Kaposi's sarcoma (KS) is highly variable, ranging from minimal stable disease to explosive growth. Although KS is primarily a cutaneous disease, extracutaneous spread is common; the oral cavity, gastrointestinal (GI) tract, lungs, and lymph nodes are often involved. The psychosocial burden associated with KS may be profound. The initial evaluation of a patient with KS consists mainly of a thorough physical examination with special attention paid to those areas typically affected by the disease, the testing of stool for occult blood, and a chest x-ray. Treatment options depend greatly on the tumor (extent of tumor and rate of growth), human immunodeficiency virus type I (HIV-I) viral load, and host factors (CD4+ T-lymphocyte count and overall medical condition). Limited cutaneous disease may be treated with topical alitretinoin gel, intralesional vinblastine, radiation therapy, laser therapy, or cryotherapy. The high benefit-to-risk ratio of liposomal anthracyclines (daunorubicin and doxorubicin) and paclitaxel have tremendously simplified the management of patients in whom systemic therapy is warranted. Additionally, epidemiologic evidence of a marked decline in new KS since the widespread use of highly active antiretroviral therapy (HAART) advocates its use. KS herpes virus/human herpes virus 8 (KSHV/HHV-8), sex hormones, and the processes of angiogenesis and cellular differentiation all serve as targets for pathogenesis-based clinical trials. Virtually all patients with KS can benefit from the many approved and investigational agents developed through years of collaborative translational and clinical research.
Sequential Evaluation of Dogs Naturally Infected withEhrlichia canis,Ehrlichia chaffeensis,Ehrlichia equi,Ehrlichia ewingii, orBartonella vinsonii (1998)

Historically, disease manifestations in dogs seroreactive to Ehrlichia canis antigens by indirect immunofluorescent antibody testing have been attributed to infection with either E. canis or Ehrlichia ewingii. A 1996 study by Dawson and colleagues provided PCR evidence that healthy dogs from southeastern Virginia could be naturally infected with Ehrlichia chaffeensis. This observation stimulated us to determine which Ehrlichia spp. infected sick dogs that were referred to our hospital from the same region. Based upon PCR amplification with species-specific primers, sick dogs seroreactive to E. canis antigens were determined to be infected with four Ehrlichia species: E. canis, E. chaffeensis, E. equi, and E. ewingii. Coinfection with three Ehrlichia species (E. canis, E. ewingii, and E. equi) was documented for one dog. An additional canine pathogen presumed to be tick transmitted, Bartonella vinsonii subsp. berkhoffii, was identified in 7 of 12 dogs. Importantly, our results indicate that in naturally infected dogs, E. chaffeensis can cause severe disease manifestations that are clinically and serologically indistinguishable from disease manifestations of E. canis or E. ewingii. In addition, our findings support the efficacy of doxycycline for treatment of E. canis, E. equi, and E. ewingii infections but indicate that, based upon the persistence of E. chaffeensis DNA for 1 year following treatment, E. chaffeensis infection in dogs may be more refractory to doxycycline treatment. Undetected coinfection with Bartonella may also complicate the evaluation of treatment efficacy while resulting in disease manifestations that mimic ehrlichiosis.
Metabolic flux analysis ofEscherichia coli expressing theBacillus subtilis acetolactate synthase in batch and continuous cultures (1999)

Metabolically engineered Escherichia coli expressing the B. subtilis acetolactate synthase has shown to be capable of reducing acetate accumulation. This reduction subsequently led to a significant enhancement in recombinant protein production. The main focus of this study is to systematically examine the effect of ALS in the metabolic patterns of E. coli in batch and continuous culture. The specific acetate production rate of a strain carrying the B. subtilis als gene is 75% lower than that of the control strain (host carrying the control plasmid pACYC184) in batch cultures. The ALS strain is further demonstrated to be capable of maintaining a reduced specific acetate production rate in continuous cultures at dilution rates ranging from 0.1 to 0.4 h-1. In addition, this ALS strain is shown to have a higher ATP yield and lower maintenance coefficient. The metabolic flux analysis of carbon flux distribution of the central metabolic pathways and at the pyruvate branch point reveals that this strain has the ability to channel excess pyruvate to the much less toxic compound, acetoin.
Refined Molecular Structure of Pig Pancreatic α-Amylase at 2·1 Å Resolution (1994)

The structure of pig pancreatic alpha-amylase has been determined by X-ray diffraction analysis using multiple isomorphous replacement in a crystal of space group P2(1)2(1)2(1) (a = 70.6 A, b = 114.8 A, c = 118.8 A) containing nearly 75% solvent. The structure was refined by simulated annealing and Powell minimization, as monitored by 2Fo-Fc difference Fourier syntheses, to a conventional R of 0.168 at 2.1 A resolution. The final model consists of all 496 amino acid residues, a chloride and a calcium ion, 145 water molecules and an endogenous disaccharide molecule that contiguously links protein molecules related by the 2(1) crystallographic operator along x. The protein is composed of a large domain (amino acid residues 1 to 403) featuring a central alpha ta-barrel of eight parallel strands and connecting helices with a prominent excursion between strand beta 3 and helix alpha 3 (amino acid residues 100 to 168). The final 93 amino acid residues at the carboxyl terminus form a second small domain consisting of a compact Greek key beta-barrel. The domains are tightly associated through hydrophobic interfaces. The beta 3/alpha 3 excursion and portions of the central alpha/beta-barrel provide four protein ligands to the tightly bound Ca ion; three water molecules complete the coordination. The Cl- ion is bound within one end of the alpha/beta-barrel by two arginine residues in a manner suggesting a plausible mechanism for its allosteric activation of the enzyme. A crystalline complex of the pancreatic alpha-amylase with alpha-cyclodextrin, a cyclic substrate analog of six glucose residues, reveals, in difference Fourier maps, three unique binding sites. One of the alpha-cyclodextrin sites is near the center of the long polysaccharide binding cleft that traverses one end of the alpha/beta-barrel, another is at the extreme of this cleft. By symmetry this can also be considered as two half sites located at the extremes of the active site cleft. This latter alpha-cyclodextrin displaces the endogenous disaccharide when it binds and, along with the first sugar ring, delineates the extended starch binding site. The third alpha-cyclodextrin binds at an "accessory site" near the edge of the protein and is quite distant from the polysaccharide binding cleft. Its presence explains the multivalency of alpha-amylase binding to dextrins in solution. The extended active site cleft is formed by large, sweeping, connecting loops at one end of the alpha/beta-barrel. These include three sequence segments that are highly conserved among alpha-amylases.(ABSTRACT TRUNCATED AT 400 WORDS)
Adjuvant immunotoxin therapy with anti-B4-blocked ricin after autologous bone marrow transplantation for patients with B-cell non- Hodgkin's lymphoma (1993)

Anti-B-blocked ricin (anti-B4-bR) combines the specificity of the anti- B4 (CD19) monoclonal antibody with the protein toxin “blocked ricin.” In blocked ricin, affinity ligands are attached to the ricin B-chain to attenuate its lectin binding capacity. In a phase I trial, Anti-B4-bR was administered by 7-day continuous infusion to 12 patients in complete remission after autologous bone marrow transplantation (ABMT) for relapsed B-cell non-Hodgkin's lymphoma (NHL). Patients were treated at 20, 40, and 50 micrograms/kg/d for 7 days. Potentially therapeutic serum levels could be sustained for 3 to 4 days. The maximum tolerated dose was 40 micrograms/kg/d for 7 days (total 280 micrograms/kg). The dose-limiting toxicities were reversible grade IV thrombocytopenia and elevation of hepatic transaminases. Mild capillary leak syndrome was manifested by hypoalbuminemia, peripheral edema (4 patients), and dyspnea (1 patient). Anti-immunotoxin antibodies developed in 7 patients. Eleven patients remain in complete remission between 13 and 26 months post-ABMT (median 17 months). These results show that Anti-B4- bR can be administered with tolerable, reversible toxicities to patients with B-cell NHL in complete remission following ABMT.
Motivation to change, coping, and self-esteem in adolescent anorexia nervosa: a validation study of the Anorexia Nervosa Stages of Change Questionnaire (ANSOCQ) (2017)

NCT02828956. Retrospectively registered July 2016.
Pulsed atomic layer epitaxy of quaternary AlInGaN layers (2001)

In this letter, we report on a material deposition scheme for quaternary AlxInyGa1−x–yN layers using a pulsed atomic layer epitaxy (PALE) technique. The PALE approach allows accurate control of the quaternary layer composition and thickness by simply changing the number of aluminum, indium, and gallium pulses in a unit cell and the number of unit cell repeats. Using PALE, AlInGaN layers with Al mole fractions in excess of 40% and strong room-temperature photoluminescence peaks at 280 nm can easily be grown even at temperatures lower than 800 °C.
Phytochromes: Photosensory Perception and Signal Transduction (1995)

The phytochrome family of photoreceptors monitors the light environment and dictates patterns of gene expression that enable the plant to optimize growth and development in accordance with prevailing conditions. The enduring challenge is to define the biochemical mechanism of phytochrome action and to dissect the signaling circuitry by which the photoreceptor molecules relay sensory information to the genes they regulate. Evidence indicates that individual phytochromes have specialized photosensory functions. The amino-terminal domain of the molecule determines this photosensory specificity, whereas a short segment in the carboxyl-terminal domain is critical for signal transfer to downstream components. Heterotrimeric GTP-binding proteins, calcium-calmodulin, cyclic guanosine 5'-phosphate, and the COP-DET-FUS class of master regulators are implicated as signaling intermediates in phototransduction.
Probing the binding mechanism and affinity of tanezumab, a recombinant humanized anti‐NGF monoclonal antibody, using a repertoire of biosensors (2008)

We describe the use of four complementary biosensors (Biacore 3000, Octet QK, ProteOn XPR36, and KinExA 3000) in characterizing the kinetics of human nerve growth factor (NGF) binding to a humanized NGF-neutralizing monoclonal antibody (tanezumab, formerly known as RN624). Tanezumab is a clinical candidate as a therapy for chronic pain. Our measurements were consistent with the NGF/tanezumab binding affinity being tighter than 10 pM due to the formation of an extremely stable complex that had an estimated half-life exceeding 100 h, which was beyond the resolution of any of our methods. The system was particularly challenging to study because NGF is an obligate homodimer, and we describe various assay orientations and immobilization methods that were used to minimize avidity in our experiments while keeping NGF in as native a state as possible. We also explored the interactions of NGF with its natural receptors, TrkA and P75, and how tanezumab blocks them. The Biacore blocking assay that we designed was used to quantify the potency of tanezumab and is more precise and reproducible than the currently available cell-based functional assays.
Lack of complex I is associated with oncocytic thyroid tumours (2009)

Oncocytic tumours are characterised by hyperproliferation of mitochondria. We immunohistochemically analysed all enzymes of the oxidative phosphorylation system in 19 oncocytic thyroid tumours. A specific lack of complex I was detected, which was expressed at <5% of the level determined in surrounding non-cancerous tissue.