gebhart/patrepeval huggingface dataset:
Marked variation in the size of genomic plasmids among members of a family of related Epstein-Barr viruses. (1992)

Epstein-Barr virus (EBV) genomes in the P3J-HR-1 (HR-1) Burkitt lymphoma cell line rearrange at a high rate. Previously described deletions and rearrangements in HR-1 cells have been found at sites of EBV replication in vivo, suggesting that DNA rearrangement may be an integral aspect of EBV biology and pathogenesis. We examined the structure of linear EBV genomes in subcultures of HR-1 cells using contour-clamped homogenous electric field gel electrophoresis. We developed a second pulsed electrophoretic technique to separate intracellular circular EBV plasmids. The standard, linear HR-1 EBV genome was approximately 155 kilobases in length. Linear molecules of less than unit length, presumably defective genomes, were seen in numerous subcultures. Linear intracellular genomes greater than 155 kilobases were also detected, but only linear genomes of 155 kilobases or less were packaged into virions. The size of circular EBV plasmids also varied greatly among HR-1 subcultures, some of which contained two plasmids of different size. The progeny of the unusual circular plasmids could be either standard or nonstandard linear genomes. No aberrant linear or circular form was detected in a subculture carrying the previously described het fragments. Pulsed-gel electrophoresis has provided two additional characteristics of mutant EBVs: abnormal linear and circular genome configurations.
Procoagulant activity on injured arteries and associated thrombi is mediated primarily by the complex of tissue factor and factor VIIa. (1996)

Procoagulant activity on injured vessels and associated thrombi is mediated by factor Xa, a product of the functional initiation of coagulation by factor VIIa associated with tissue factor. Accordingly, inhibition of tissue factor-mediated coagulation may be effective for attenuation of active thrombogenesis on injured vessels and during thrombolysis.
Disk Scheduling Revisited (1990)

Since the invention of the movable head disk, people have improved I/O performance by intelligent scheduling of disk accesses. We have applied these techniques to systems with large memories and potentially long disk queues. By viewing the entire buffer cache as a write buffer, we can improve disk bandwidth utilization by applying some traditional disk scheduling techniques. We have analyzed these techniques, which attempt to optimize head movement and guarantee fairness in response time, in the presence of long disk queues. We then propose two algorithms which take rotational latency into account, achieving disk bandwidth utilizations of nearly four times a simple first come first serve algorithm. One of these two algorithms, a weighted shortest total time first, is particularly applicable to a file server environment because it guarantees that all requests get to disk within a specified time window. 1. Introduction Present day magnetic disks are capable of providing I/O bandwidth on...
Refined solution structure and backbone dynamics of HIV‐1 Nef (1997)

The tendency of HIV-1 Nef to form aggregates in solution, particularly at pH values below 8, together with its large fraction of highly mobile residues seriously complicated determination of its three-dimensional structure, both for heteronuclear solution NMR (Grzesiek et al., 1996a, Nat Struct Biol 3:340-345) and for X-ray crystallography (Lee et al., 1996, Cell 85:931-942). Methods used to determine the Nef structure by NMR at pH 8 and 0.6 mM concentration are presented, together with a detailed description of Nef's secondary and tertiary structure. The described techniques have general applicability for the NMR structure determination of proteins that are aggregating and/or have limited stability at low pH values. Extensive chemical shift assignments are reported for backbone and side chain 1H, 13C, and 15N resonances of the HIV-1 Nef deletion mutants NEF delta 2-39, NEF delta 2-39, delta 159-173, and of NEF delta 2-39, delta 159-173 in complex with the SH3 domain of the Hck tyrosine protein kinase. Besides a type II polyproline helix, Nef's structure consists of three alpha-helices, a 3(10) helix, and a five-stranded anti-parallel beta-sheet. The analysis of 15N relaxation parameters of the backbone amide sites reveals that all the secondary structure elements are non-mobile on the picosecond to nanosecond and on the millisecond time scale. A large number of slowly exchanging amide protons provides evidence for the stability of the Nef core even on the time scale of hours. Significant internal motions on the ps to ns time scale are detected for residues 60 to 71 and for residues 149 to 180, which form solvent-exposed loops. The residues of the HIV-1 protease cleavage site (W57/L58) do not exhibit large amplitude motions on the sub-nanosecond time scale, and their side chains insert themselves into a hydrophobic crevice formed between the C-terminus of helix 1 and the N-terminus of helix 2. A refined structure has been determined based on additional constraints for side-chain and backbone dihedral angles derived from a large number of three-bond J-coupling and ROE data.
Manganese as a Substitute for Rhenium in CO2 Reduction Catalysts: The Importance of Acids (2013)

Electrocatalytic properties, X-ray crystallographic studies, and infrared spectroelectrochemistry (IR-SEC) of Mn(bpy-tBu)(CO)3Br and [Mn(bpy-tBu)(CO)3(MeCN)](OTf) are reported. Addition of Brönsted acids to CO2-saturated solutions of these Mn complexes and subsequent reduction of the complexes lead to the stable and efficient production of CO from CO2. Unlike the analogous Re catalysts, these Mn catalysts require the addition of Brönsted acids for catalytic turnover. Current densities up to 30 mA/cm(2) were observed during bulk electrolysis using 5 mM Mn(bpy-tBu)(CO)3Br, 1 M 2,2,2-trifluoroethanol, and a glassy carbon working electrode. During bulk electrolysis at -2.2 V vs SCE, a TOF of 340 s(-1) was calculated for Mn(bpy-tBu)(CO)3Br with 1.4 M trifluoroethanol, corresponding to a Faradaic efficiency of 100 ± 15% for the formation of CO from CO2, with no observable production of H2. When compared to the analogous Re catalysts, the Mn catalysts operate at a lower overpotential and exhibit similar catalytic activities. X-ray crystallography of the reduced species, [Mn(bpy-tBu)(CO)3](-), shows a five-coordinate Mn center, similar to its rhenium analogue. Three distinct species were observed in the IR-SEC of Mn(bpy-tBu)(CO)3Br. These were of the parent Mn(bpy-tBu)(CO)3Br complex, the dimer [Mn(bpy-tBu)(CO)3]2, and the [Mn(bpy-tBu)(CO)3](-) anion.
Nosocomial transmission of respiratory syncytial virus in immunocompromised adults (1991)

Respiratory syncytial virus (RSV) isolates obtained from nine infected immunocompromised adult patients hospitalized during two consecutive winters (January through April 1987 and 1988) were collected and analyzed against a panel of monoclonal antibodies by an enzyme immunoassay. The history of the patients' illness, onset of symptoms, and date of initial isolation of virus was correlated with the hospital ward and time of hospitalization. Three patients died of respiratory failure related to RSV infection acquired nosocomially. A cluster of RSV disease in four patients hospitalized simultaneously during the 1987 season was demonstrated to be caused by four antigenically distinct viruses; despite an epidemiologic link among the patients, each had been infected from a different source. The RSV disease in the five immunocompromised adults in 1988 was caused by two distinct strains; three patients were infected with RSV subgroup A/4, and two were infected with RSV subgroup B/2. Combining the epidemiologic and strain characterization studies, none of four patients in 1987 were infected from each other, and two of five patients in 1988 may have been infected, directly or indirectly, from one of the other five. The strain characterization studies demonstrated the potential complexity of RSV nosocomial transmission and the need to consider a number of sources for transmission in developing effective prevention strategies. The three deaths underscore the importance of nosocomial RSV disease and the importance of effective prevention strategies.
RRM1 and PTEN As Prognostic Parameters for Overall and Disease-Free Survival in Patients With Non–Small-Cell Lung Cancer (2004)

RRM1 is a biologically and clinically important determinant of malignant behavior in NSCLC. Knowing the level of expression of this gene adds significant information to management decisions independent of the currently used outcome predictors of tumor stage, performance status, and weight loss. Future clinical trials should stratify patients based on expression of this gene to avoid unwanted biases.
Activity of intrathecal 4-hydroperoxycyclophosphamide in a nude rat model of human neoplastic meningitis. (1990)

Neoplastic meningitis can result from leptomeningeal dissemination of a variety of cancers. We now report the development of animal models of human neoplastic meningitis and activity of intrathecal 4-hydroperoxycyclophosphamide (4-HC) against the human rhabdomyosarcoma cell line TE-671 and the human glioma cell line D-54 MG grown in the subarachnoid space of athymic rats. The injection of 5 x 10(5) TE-671 or D-54 MG cells resulted in leptomeningeal tumor growth from the base of the brain to the cauda equina. Daily weights and neurological examinations revealed progressive neurological deficits and weight loss, with death occurring between Days 21 and 27 for TE-671 and Days 14 and 26 for D-54 MG. 4-HC toxicity in non-tumor-bearing rats was assessed at dose levels of 2.0, 10.0, 15.0, and 20.0 mM, with clinical and histological evidence of neurotoxicity observed at the 2 highest dose levels. Intrathecal treatment with 4-HC on Day 8 following injection of TE-671 resulted in an increase in median survival of 20% (P = 0.04) at 1.0 mM 4-HC and 41% (P less than 0.001) at 2.5 mM 4-HC. Intrathecal treatment with 4-HC (2.5 mM) on Day 5 following injection of D-54 MG resulted in an increase in median survival of 23% (P = 0.009). These studies show the usefulness of the athymic rat model of human neoplastic meningitis and demonstrate the efficacy in vivo of intrathecally administered 4-HC against a human glioma and a human rhabdomyosarcoma cell line and the lack of toxicity at therapeutic levels of 4-HC in normal athymic rats.
Pharmaceutical salts: Theory, use in solid dosage forms and in situ preparation in an aerosol (2016)

In this article, the theoretical foundation for salts is given with an emphasis on the amount of drug in solution. Consideration is given for the solubility of the non-ionized form, acid dissociation constant and solubility product, which are the limiting constraints. For dissolution of nonionized drugs, the surface pH differs from the bulk pH, giving rise to a lower than expected rate. For salts, theoretical considerations are relatively complex, and an experimental approach to estimating the surface pH is more likely to be of value in predicting the dissolution rate. General guidelines are described for screening, preparing and characterizing drugs as salts, which critically depend on the goal of the product development. Thereafter, our work involving the preparation of salts as a means to generate aerosols from a solution is provided. The solubility of six structurally related compounds was determined in four acids. Thereafter, the amount of the compound in solution was determined as a function of pH, using the acid that provided the highest solubility. Because the pH required to achieve the needed concentration for aerosol generation was low, ammonia vapor was introduced into the air stream to neutralize aerosol droplets. Solvent was then removed from the aerosol by a silica column. The resulting aerosol had a concentration of 96 µg/l and a mass median particle size of 1.8 µm. The reported pharmacokinetic study substantiated the feasibility of evaluating its safety and efficacy of inhalation administration in the rat model.
Dimethyl Sulfoxide Has an Impact on Epigenetic Profile in Mouse Embryoid Body (2006)

Dimethyl sulfoxide (DMSO), an amphipathic molecule, is widely used not only as a solvent for water-insoluble substances but also as a cryopreservant for various types of cells. Exposure to DMSO sometimes causes unexpected changes in cell fates. Because mammalian development and cellular differentiation are controlled epigenetically by DNA methylation and histone modifications, DMSO likely affects the epigenetic system. The effects of DMSO on transcription of three major DNA methyltransferases (Dnmts) and five well-studied histone modification enzymes were examined in mouse embryonic stem cells and embryoid bodies (EBs) by reverse transcription-polymerase chain reaction. Addition of DMSO (0.02%-1.0%) to EBs in culture induced an increase in Dnmt3a mRNA levels with increasing dosage. Increased expression of two subtypes of Dnmt3a in protein levels was confirmed by Western blotting. Southern blot analysis revealed that DMSO caused hypermethylation of two kinds of repetitive sequences in EBs. Furthermore, restriction landmark genomic scanning, by which DNA methylation status can be analyzed on thousands of loci in genic regions, revealed that DMSO affected DNA methylation status at multiple loci, inducing hypomethylation as well as hypermethylation depending on the genomic loci. In conclusion, DMSO has an impact on the epigenetic profile: upregulation of Dnmt3a expression and alteration of genome-wide DNA methylation profiles with phenotypic changes in EBs.
Antigenic variation of human and bovine parainfluenza virus type 3 strains (1990)

Three human and six bovine parainfluenza virus type 3 (PIV3) strains were examined by the use of 60 monoclonal antibodies (MAbs). Fifty-three MAbs to the human C243 strain were directed against six, four, nine and seven epitopes of the haemagglutinin-neuraminidase (HN), fusion (F), nucleocapsid (N) and matrix proteins, respectively. Seven MAbs to the bovine strain were directed against three epitopes of the HN protein and three epitopes of the F protein. Each strain was characterized in ELISA and immunofluorescence tests with all MAbs and in a haemagglutination inhibition assay with the anti-HN MAbs. There were marked differences between human and bovine viruses, primarily in the HN protein where five epitopes differed. One epitope of the F and one of the N protein also differed. Bovine PIV3 was found to be a homogeneous subtype and distinct from human PIV3.
Clinical, Histopathologic, and Genomic Features of Spitz Tumors With ALK Fusions (2015)

Activating kinase fusions have recently been described as early oncogenic events that are mutually exclusive with HRAS and BRAF mutations in Spitz tumors. Here, we report a series of 32 Spitz tumors with ALK fusions (6 Spitz nevi, 22 atypical Spitz tumors, and 4 spitzoid melanomas) in patients ranging from 5 months to 64 years (median=12 y) of age. The tumors typically presented as exophytic papules on the extremities and were occasionally darkly pigmented. In addition to ALK fusions previously described in other tumor types (NPM1-ALK, TPR-ALK), we identified 2 novel ALK fusions (CLIP1-ALK and GTF3C2-ALK) in our cohort of Spitz tumors. Array comparative genomic hybridization of 19 of these tumors demonstrated a high frequency of chromosome 2 aberrations (where ALK resides, 63%) and chromosome 1p loss in 37% of the cases. Spitz tumors with ALK fusions demonstrated unique histopathologic features. Clefts and small vesicle-like spaces were arrayed between plump spindled melanocytes with fibrillar cytoplasm and enlarged nuclei. These melanocytes were typically arrayed in elongated and fusiform nests with radial orientation. The tumors often had extension into the dermis or subcutis with a wedge-shaped or bulbous lower border (45% and 17%, respectively). An infiltrative growth pattern was often present at the periphery of the tumor and was highlighted by ALK immunohistochemistry. In conclusion, Spitz tumors with ALK rearrangement show distinct histopathologic features that should aid in improving classification of these diagnostically challenging tumors.
Biimidazole complexes of ML22+ [M = Ru or Os, L = 2-(phenylazo)pyridine]. Synthesis, structure and redox properties of mono- and di-nuclear complexes ‡ (1998)

A series of mono- and di-nuclear complexes of ruthenium and osmium containing the terminal ligands 2-(phenylazo)pyridine (pap), 2,2′-bipyridine (bpy) and the bridging ligand 2,2′-biimidazole(H2biim) have been prepared. The mononuclear complex [Ru(pap)2(H2biim)][ClO4]2·3CH2Cl2 was characterised by a single-crystal structure determination. The mononuclear complexes [M(pap)2(H2biim)]2+ (M = Ru or Os) act as dibasic acids and undergo deprotonation to afford [M(pap)2(Hbiim)]+ and [M(pap)2(biim)]. The completely deprotonated complexes behave as reactive building units (‘metal complex as ligand’) which react smoothly with metal complex units to produce homo- and hetero-dinuclear complexes. The structure of the dinuclear complex [Ru2(bpy)4(biim)][ClO4]2 was determined. Cyclic voltammetric studies on the above complexes were performed. The quasi-reversible half-wave potentials of the oxidation processes of the dinuclear complexes are dependent on the metal as well as on the nature of the terminal ligands. These undergo two one-electron oxidation processes centered at the metal. Partial oxidation of the dinuclear complexes led to unsymmetrical bridge cleavage to form monomeric complexes. Large numbers of ligand reduction responses were observed. In some cases the first ligand reduction occurs close to zero potential (with respect to the SCE).
Microfabricated atomic vapor cell arrays for magnetic field measurements (2011)

We describe a method for charging atomic vapor cells with cesium and buffer gas. By this, it is possible to adjust the buffer gas pressure in the cells with good accuracy. Furthermore, we present a new design of microfabricated vapor cell arrays, which combine silicon wafer based microfabrication and ultrasonic machining to achieve the arrays of thermally separated cells with 50 mm(3) volume. With cells fabricated in the outlined way, intrinsic magnetic field sensitivities down to 300 fT∕Hz(1∕2) are reached.
TRPM7 Provides an Ion Channel Mechanism for Cellular Entry of Trace Metal Ions (2002)

Trace metal ions such as Zn(2+), Fe(2+), Cu(2+), Mn(2+), and Co(2+) are required cofactors for many essential cellular enzymes, yet little is known about the mechanisms through which they enter into cells. We have shown previously that the widely expressed ion channel TRPM7 (LTRPC7, ChaK1, TRP-PLIK) functions as a Ca(2+)- and Mg(2+)-permeable cation channel, whose activity is regulated by intracellular Mg(2+) and Mg(2+).ATP and have designated native TRPM7-mediated currents as magnesium-nucleotide-regulated metal ion currents (MagNuM). Here we report that heterologously overexpressed TRPM7 in HEK-293 cells conducts a range of essential and toxic divalent metal ions with strong preference for Zn(2+) and Ni(2+), which both permeate TRPM7 up to four times better than Ca(2+). Similarly, native MagNuM currents are also able to support Zn(2+) entry. Furthermore, TRPM7 allows other essential metals such as Mn(2+) and Co(2+) to permeate, and permits significant entry of nonphysiologic or toxic metals such as Cd(2+), Ba(2+), and Sr(2+). Equimolar replacement studies substituting 10 mM Ca(2+) with the respective divalent ions reveal a unique permeation profile for TRPM7 with a permeability sequence of Zn(2+) approximately Ni(2+) >> Ba(2+) > Co(2+) > Mg(2+) >/= Mn(2+) >/= Sr(2+) >/= Cd(2+) >/= Ca(2+), while trivalent ions such as La(3+) and Gd(3+) are not measurably permeable. With the exception of Mg(2+), which exerts strong negative feedback from the intracellular side of the pore, this sequence is faithfully maintained when isotonic solutions of these divalent cations are used. Fura-2 quenching experiments with Mn(2+), Co(2+), or Ni(2+) suggest that these can be transported by TRPM7 in the presence of physiological levels of Ca(2+) and Mg(2+), suggesting that TRPM7 represents a novel ion-channel mechanism for cellular metal ion entry into vertebrate cells.
Rhodacyanine dye MKT-077 inhibits in vitro telomerase assay but has no detectable effects on telomerase activity in vivo. (2002)

MKT-077, a cationic rhodacyanine dye analogue, causes selective toxicity to cancer cells. Its cellular targets elucidated thus far include oncogenic Ras, F-actin, mortalin (hmot-2)/mthsp70, and telomerase. Here we report that MKT-077 causes growth arrest of cancer cells in culture independent of their Ras, p53, or telomerase status. Telomerase activity is inhibited in vitro by MKT-077 in the telomerase assay used. However, the in vivo toxicity seen in telomerase-positive cancer cells was not accompanied by inhibition of telomerase activity or telomere shortening. Furthermore, cells with an alternative mechanism for lengthening of telomeres were also sensitive to MKT-077 and showed enhanced formation of alternative mechanism for lengthening of telomeres-associated PML bodies in their nuclei. The data suggested that inhibition of telomerase activity is unlikely to be a prime cause of MKT-077-induced toxicity in cancer cells.
Anandamide amidohydrolase reacting with 2‐arachidonoylglycerol, another cannabinoid receptor ligand (1998)

Two endogenous ligands for cannabinoid receptors, anandamide (arachidonylethanolamide) and 2-arachidonoylglycerol, lose their biological activities by enzymatic hydrolysis. A cDNA for a rat liver enzyme hydrolyzing anandamide as well as oleamide was overexpressed in COS-7 cells. When the particulate fraction was allowed to react with 2-arachidonoylglycerol, arachidonic acid was produced. In contrast, this hydrolytic reaction did not occur with the control cells. The hydrolysis of 2-arachidonoylglycerol proceeded about 4-fold faster than the anandamide hydrolysis with a Km value as low as 6 microM and an optimal pH of 10. Phenylmethylsulfonyl fluoride and methyl arachidonyl fluorophosphonate inhibited the hydrolysis of both anandamide and 2-arachidonoylglycerol in parallel. Furthermore, the hydrolysis of [14C]2-arachidonoylglycerol was inhibited by anandamide dose-dependently. These results suggest that anandamide and 2-arachidonoylglycerol can be inactivated by the same enzyme.
Environmental Transport Processes (2012)

Equilibrium Calculations Diffusive Transport The Constitutive Transport Equation Concentration Profiles and Chemical Fluxes Mass Transport Coefficients: From Theory to Empiricism Chemical Transport in Sheared Reactors Suspended Unattached and Aggregated Microorganisms Biofilms Dispersion Rivers, Lakes, and Oceans Chemical Transport in Porous Media Particles and Fractals Coagulation in Natural and Engineered Systems Particle Transport in Porous Media Appendices Index.
High-Speed Spectroscopic Transient Absorption Imaging of Defects in Graphene (2018)

Graphene grain boundaries (GBs) and other nanodefects can deteriorate electronic properties. Here, using transient absorption (TA) microscopy we directly visualized GBs by TA intensity increase due to change in density of state. We also observed a faster decay due to defect-accelerated carrier relaxation in the GB area. By line-illumination and parallel detection, we increased the TA intensity imaging speed to 1000 frames per second, which is 6 orders of magnitude faster than Raman microscopy. Combined with a resonant optical delay tuner which scans a 5.3 ps temporal delay within 92 μs, our system enabled spectroscopic TA imaging, at a speed of 50 stacks per second, to probe and characterize graphene nanodefects based on the TA decay rate. Finally, we demonstrate real-time nondestructive characterization of graphene at a rolling speed of 0.3 m/min, which matches the fastest roll-to-roll manufacturing process reported.