gebhart/patrepeval huggingface dataset:
Characterization of Tn904 insertions in octopine Ti plasmid mutants of Agrobacterium tumefaciens (1980)

Seven Tn904 insertion mutants of pTi Ach5 affecting Agrobacterium tumefaciens virulence were studied. The mutant character was shown to be plasmid borne. Four of these mutants were avirulent and carried an insertion in restriction endonuclease HpaI fragment 12, a 3.3-megadalton fragment, which therefore appears to be a Ti plasmid region essential for virulence. Two mutants were attenuated in virulence. The inserts mapped close to HpaI fragment 12. One mutant giving rise to small tumors with excessive adventitious root formation on Kalanchoe daigremontiana carried an insertion in the right side of the common sequence in the deoxyribonucleic acid of the Ti plasmid detected in crown gall tumors. The insertion behavior of Tn904 was studied by analyzing 11 independently isolated and randomly chosen mutants. The Tn904 inserts did not affect oncogenicity, tumor morphology, bacterial transfer functions, octopine catabolism functions, or vital parts of the Ti plasmid, such as the origin of replication. Most of the Tn904 inserts were concentrated in a small part of the map. The size of additional deoxyribonucleic acid as a result of Tn904 inserts varied between 5 and 15 megadaltons. In two cases a Ti plasmid was found with two Tn904 insertions at different positions.
Quantitative analysis of DNA orientation in stationary AC electric fields using fluorescence anisotropy (1998)

Previous investigations into DNA orientation under an electrostatic field used either a low-intensity or a pulsed field, and the measurements were made in the region where the degree of orientation was relatively low. This was because applying high-intensity steady fields to aqueous solutions resulted in a temperature rise and caused turbulence or boiling, which interfered with orientation. In this paper, microfabricated electrodes are used to obtain stationary AC electric fields in excess of 1 MV/m. Planar microelectrodes with either 15- or 60-/spl mu/m gaps, depending on the length of sample DNA to be used, are fabricated with planar technique on glass substrates. Because the high-field region in the gap is small and has a high surface-to-volume ratio, Joule heat is efficiently removed, so that a very high-intensity field can be created without excessive temperature rise. A high-sensitivity detection method is required for measurements with microelectrodes, due to the small number of molecules involved. For this purpose, a fluorescent dye is intercalated into the bases of the DNA, and the optical polarization of emitted fluorescence is measured. The polarization components of the emitted light, both parallel and perpendicular to the applied electrostatic field, are measured independently, and fluorescent anisotropy, the ratio of the difference between parallel and perpendicular polarization to total emission, is used as an index of DNA orientation.
MALDI-MS Direct Tissue Analysis of Proteins:  Improving Signal Sensitivity Using Organic Treatments (2006)

Direct tissue analysis using MALDI-MS allows the generation of profiles while maintaining the integrity of the tissue, displaying cellular localizations and avoiding tedious extraction and purification steps. However, lower spectral quality can result from direct tissue analysis due to variations in section thickness, the nature of the tissue, and the limited access to peptides/proteins due to high lipid content. To improve signal sensitivity, we have developed a tissue-washing procedure using organic solvents traditionally used for lipid extraction, i.e., CHCl3, hexane, toluene, acetone, and xylene. The increased detection for peptides/proteins (m/z 5000-30,000) is close to 40% with chloroform or xylene, and 25% with hexane, while also improving sample reproducibility for each solvent used in the present study. This strategy improved matrix cocrystallization with tissue peptides/proteins and more importantly with cytoplasmic proteins without delocalization. The extracted lipids were characterized by nanoESI-QqTOF/MS/MS using the precursor ion mode, lithium adducts, or both and were identified as phospholipids including phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, and lysophosphatidylinositol, confirming membrane lipid extraction from the tissues.
Polarization Multiplexing With the Kramers-Kronig Receiver (2017)

We present two schemes extending the Kramers-Kronig-receiver to polarization multiplexed transmission. One of the schemes relies on the Stokes receiver and allows for complex-valued polarization multiplexed transmission without using a local oscillator, and active polarization control at the receiver. It uses three photodiodes and requires three analog-to-digital converters (ADCs). The other scheme uses a local oscillator, and its implementation is suitable in all cases where the transmitter and the receiver operate at the same wavelength, so that the local oscillator signal can be extracted from the transmit laser. It uses only two photodiodes and two ADCs, and does not require optical hybrids. The performance of the first (Stokes-based) scheme is studied numerically, whereas that of the second scheme is studied both numerically and experimentally.
Rho Family Proteins Modulate Rapid Apoptosis Induced by Cytotoxic T Lymphocytes and Fas (2000)

Little is known about the role of Rho proteins in apoptosis produced by stimuli evolved specifically to produce apoptosis, such as granzymes from cytotoxic T lymphocytes (CTLs) and Fas. Here we demonstrate that all three Rho family members are involved in CTL- and Fas-induced killing. Dominant-negative mutants of each Rho family member and Clostridium difficile toxin B, an inhibitor of all family members, strongly inhibited the susceptibility of cells to CTL- and Fas-induced apoptosis. Fas-induced caspase-3 activation was inhibited by C. difficile toxin. Activated mutants of each GTPase increased susceptibility to apoptosis, and activation of Cdc42 increased within 5 min of Fas stimulation. In contrast, during the time required for CTL and Fas killing, no apoptosis was produced by dominant-negative or activated mutants or by C. difficile toxin alone. Inhibition of actin polymerization using latrunculin A reduced the ability of constitutively active GTPase mutants to stimulate apoptosis and blocked Fas-induced activation of caspase-3. Furthermore, the ability of Rac to enhance apoptosis was decreased by point mutations reported to block Rac induction of actin polymerization. Rho family proteins may regulate apoptosis through their effects on the actin cytoskeleton.
Preclinical MRI-Guided Focused Ultrasound: A Review of Systems and Current Practices (2016)

Effective preclinical research is a vital component in the development of MRI-guided focused ultrasound (MRgFUS) and its translation to clinic. In this review, we seek to outline the challenges at hand for effective preclinical research, survey different solutions, and underline best practices. Furthermore, we summarize efforts to build and characterize dedicated preclinical MRgFUS equipment, including lab prototypes and available commercial products. Finally, we discuss constraints and considerations specific to using clinical MRgFUS equipment in preclinical research. Specifically, we examine additional hardware that has been used to adapt clinical MRgFUS equipment to better position, constrain, and image preclinical subjects, as well as software solutions that have been used to extend the potential and capabilities of clinical devices.
Curved CCD detector devices and arrays for multispectral astrophysical applications and terrestrial stereo panoramic cameras (2004)

The emergence of curved CCD detectors as individual devices or as contoured mosaics assembled to match the curved focal planes of astronomical telescopes and terrestrial stereo panoramic cameras represents a major optical design advancement that greatly enhances the scientific potential of such instruments. In altering the primary detection surface within the telescope’s optical instrumentation system from flat to curved, and conforming the applied CCD’s shape precisely to the contour of the telescope’s curved focal plane, a major increase in the amount of transmittable light at various wavelengths through the system is achieved. This in turn enables multi-spectral ultra-sensitive imaging with much greater spatial resolution necessary for large and very large telescope applications, including those involving infrared image acquisition and spectroscopy, conducted over very wide fields of view. For earth-based and space-borne optical telescopes, the advent of curved CCD’s as the principle detectors provides a simplification of the telescope’s adjoining optics, reducing the number of optical elements and the occurrence of optical aberrations associated with large corrective optics used to conform to flat detectors. New astronomical experiments may be devised in the presence of curved CCD applications, in conjunction with large format cameras and curved mosaics, including three dimensional imaging spectroscopy conducted over multiple wavelengths simultaneously, wide field real-time stereoscopic tracking of remote objects within the solar system at high resolution, and deep field survey mapping of distant objects such as galaxies with much greater multi-band spatial precision over larger sky regions. Terrestrial stereo panoramic cameras equipped with arrays of curved CCD’s joined with associative wide field optics will require less optical glass and no mechanically moving parts to maintain continuous proper stereo convergence over wider perspective viewing fields than their flat CCD counterparts, lightening the cameras and enabling faster scanning and 3D integration of objects moving within a planetary terrain environment. Preliminary experiments conducted at the Sarnoff Corporation indicate the feasibility of curved CCD imagers with acceptable electro-optic integrity. Currently, we are in the process of evaluating the electro-optic performance of a curved wafer scale CCD imager. Detailed ray trace modeling and experimental electro-optical data performance obtained from the curved imager will be presented at the conference.
Systemic Tofacitinib Concentrations in Adult Patients With Atopic Dermatitis Treated With 2% Tofacitinib Ointment and Application to Pediatric Study Planning (2018)

Atopic dermatitis is a chronic eczematous, pruritic, inflammatory skin condition affecting children and adults. Tofacitinib is a Janus kinase inhibitor. The efficacy, safety, and pharmacokinetics of 2% tofacitinib ointment twice daily have been evaluated in a 4-week phase 2a multisite randomized, double-blind, vehicle-controlled, parallel-group study (NCT02001181) in adult patients with mild to moderate atopic dermatitis and 2% to 20% body surface area (BSA) involvement. Tofacitinib ointment demonstrated significantly greater efficacy versus vehicle for all efficacy end points and had an acceptable safety profile. Predose and postdose pharmacokinetic samples were collected in week 2 and week 4. The objective of this analysis was to assess if predicted mean tofacitinib concentrations with topical application at higher treated BSA across age groups would exceed relevant concentration thresholds based on oral doses of tofacitinib. In this analysis, the pharmacokinetic concentrations were characterized using a linear mixed-effects model. The model was used to predict concentrations for adults with higher (>20%) treatable BSA. Adult concentrations were used to extrapolate concentrations to a pediatric population (2 to 17 years) using allometric principles. The predicted systemic concentrations for 2% tofacitinib ointment in both adult and pediatric populations at treated BSA ≤50% for a mild to moderate atopic dermatitis population did not exceed those reported for the 10th percentile of observed oral tofacitinib 5-mg twice-daily doses in patients with moderate to severe plaque psoriasis. The methodology described will enable analysis and prediction of systemic concentrations for topical agents.
In Vitro Activities of a New Lipopeptide Antifungal Agent, FK463, against a Variety of Clinically Important Fungi (2000)

The in vitro antifungal activity and spectrum of FK463 were compared with those of amphotericin B, fluconazole, and itraconazole by using a broth microdilution method specified by National Committee for Clinical Laboratory Standards document M27-A (National Committee for Clinical Laboratory Standards, Wayne, Pa., 1997). FK463 exhibited broad-spectrum activity against clinically important pathogens including Candida species (MIC range, <==0.0039 to 2 microg/ml) and Aspergillus species (MIC range, <==0.0039 to 0.0313 microg/ml), and its MICs for such fungi were lower than those of the other antifungal agents tested. FK463 was also potently active against azole-resistant Candida albicans as well as azole-susceptible strains, and there was no cross-resistance with azoles. FK463 showed fungicidal activity against C. albicans, i.e., a 99% reduction in viability after a 24-h exposure at concentrations above 0.0156 microg/ml. The minimum fungicidal concentration (MFC) assays indicated that FK463 was fungicidal against most isolates of Candida species. In contrast, the MFCs of FK463 for A. fumigatus isolates were much higher than the MICs, indicating that its action is fungistatic against this species. FK463 had no activity against Cryptococcus neoformans, Trichosporon species, or Fusarium solani. Neither the test medium (kind and pH) nor the inoculum size greatly affected the MICs of FK463, while the addition of 4% human serum albumin increased the MICs for Candida species and A. fumigatus more than 32 times. Results from preclinical in vitro evaluations performed thus far indicate that FK463 should be a potent parenteral antifungal agent.
The Electrochemical Behavior of Alkali and Alkaline Earth Metals in Nonaqueous Battery Systems—The Solid Electrolyte Interphase Model (1979)

It is suggested that in practical nonaqueous battery systems the alkali and alkaline earth metals are always covered by a surface layer which is instantly formed by the reaction of the metal with the electrolyte. This layer, which acts as an interphase between the metal and the solution, has the properties of a solid electrolyte. The corrosion rate of the metal, the mechanism of the deposition‐dissolution process, the kinetic parameters, the quality of the metal deposit, and the half‐cell potential depend on the character of the solid electrolyte interphase (SEI).
The interferon-dependent orchestration of innate and adaptive immunity after transplantation (2012)

The therapeutic GVL effect after allogeneic stem cell transplantation is limited by the development of GVHD. The ultimate aim of current research is to separate the 2 processes in a meaningful fashion. The IFNs are a pleiotropic group of cytokines that were originally recognized because of their ability to interfere with viral replication. However, it is now established that these cytokines play an important role in orchestrating both innate and adaptive immunity. Multiple studies have investigated the effects of both types I and II IFN on GVHD and GVL in preclinical transplant models. The results indicate variable effects that are dependent on the period of activity within the developing immune response, the presence and type of pretransplant conditioning and the differential mechanisms, and IFN sensitivity of immune pathology within individual target organs during GVHD. This Perspective discusses the current literature on the IFNs and their potential modulation within clinical transplantation, focusing particularly on enhancing the therapeutic GVL effects.
Nucleotide sequence of classical swine fever virus strain Alfort/187 and transcription of infectious RNA from stably cloned full-length cDNA (1996)

The complete nucleotide sequence of the genome of classical swine fever virus (CSFV) strain Alfort/187 was determined from three cDNA libraries constructed by cloning of DNA fragments obtained from independent sets of reverse transcription and PCR. The cDNA fragments were then assembled and inserted downstream of a T7 promoter in a P15A-derived plasmid vector to obtain the full-length cDNA clone pA187-1. The first nucleotide of the CSFV genome was positioned at the transcription start site of the T7 promoter. Cleavage at an SrfI restriction site introduced at the exact 3' end of the cloned viral cDNA allowed the in vitro synthesis of full-length viral RNA by runoff transcription. This RNA proved to be infectious after transfection into porcine kidney cells. Infectivity was not increased after capping of the synthetic RNA. Virus recovered from transfected cells was titrated in porcine kidney cells by endpoint dilution using indirect immunofluorescence and a CSFV-specific monoclonal antibody. RNA transcripts generated from plasmid DNA isolated from bacteria which had been cultured and cloned 10 times remained infectious, indicating that the full-length clone is stable in bacterial cells. A silent point mutation introduced at position 11842 of the genome was retained in the recombinant virus recovered from transfected cells. An infectious chimeric construct was obtained by replacing a 696-bp fragment in pA187-1 with the corresponding cDNA fragment from the CSFV strain CAP. The stably cloned full-length CSFV cDNA allows site-specific mutagenesis of the viral genome and thus will be useful for detailed molecular characterization of the virus as well as for studies of viral pathogenesis.
Krüppel-associated box-mediated repression of RNA polymerase II promoters is influenced by the arrangement of basal promoter elements. (1996)

The evolutionarily conserved Krüppel-associated box (KRAB) is present in the N-terminal regions of more than one-third of all Krüppel-class zinc finger proteins. Recent experiments have demonstrated that the KRAB-A domain tethered to a promoter DNA by connecting to heterologous DNA-binding protein domain or targeted to a promoter-proximal RNA sequence acts as a transcriptional silencing of RNA polymerase II promoters. Here we show that expression of KRAB domain suppresses in vivo the activating function of various defined activating transcription factors, and we demonstrate that the KRAB domain specifically silences the activity of promoters whose initiation is dependent on the presence of a TATA box. Promoters whose accurate transcription initiation is directed by a pyrimidine-rich initiator element, however, are relatively unaffected. We also report in vitro transcription experiments indicating that the KRAB domain is able to repress both activated and basal promoter activity. Thus, the KRAB domain appears to repress the activity of certain promoters through direct communication with TATA box-dependent basal transcription machinery.
Anhydrotrypsin: New Features in Ligand Interactions Revealed by Affinity Chromatography and Thionine Replacement1 (1977)

Anhydrotrypsin was isolated in high purity from the product of base elimination from phenylmethanesulfonyl-trypsin, by a single operation of affinity chromatography. The adsorbent used for the chromatography was an agarose derivative coupled with peptides containing C-terminal arginine residues. As the affinity of the adsorbent for anhydrotrypsin was high compared with that for trypsin, purification of the enzyme derivative was easily achieved without the prior inactivation of trypsin which had been regenerated during the elimination reaction. Comparative studies of the ligand interaction specificities with anhydrotrypsin and trypsin confirmed the stronger interaction of the former protein with product-type ligands such as Bz-Arg-OH. No marked differences were observed between them in affinities toward substrate-type ligands such as Bz-Arg-NH2. The higher affinity of anhydrotrypsin was found to be limited to product-type ligands of L-configuration, i.e., the protein displayed an ability to discriminate the L-ligand from its optical isomer. THE PKa value for the ionization form of anhydrotrypsin responsible for the interaction with Bz-Arg-OH was estimated to be 7.60+/-0907
Potential clinical relevance of the ‘little brain’ on the mammalian heart (2007)

It is hypothesized that the heart possesses a nervous system intrinsic to it that represents the final relay station for the co-ordination of regional cardiac indices. This 'little brain' on the heart is comprised of spatially distributed sensory (afferent), interconnecting (local circuit) and motor (adrenergic and cholinergic efferent) neurones that communicate with others in intrathoracic extracardiac ganglia, all under the tonic influence of central neuronal command and circulating catecholamines. Neurones residing from the level of the heart to the insular cortex form temporally dependent reflexes that control overlapping, spatially determined cardiac indices. The emergent properties that most of its components display depend primarily on sensory transduction of the cardiovascular milieu. It is further hypothesized that the stochastic nature of such neuronal interactions represents a stabilizing feature that matches cardiac output to normal corporal blood flow demands. Thus, with regard to cardiac disease states, one must consider not only cardiac myocyte dysfunction but also the fact that components within this neuroaxis may interact abnormally to alter myocyte function. This review emphasizes the stochastic behaviour displayed by most peripheral cardiac neurones, which appears to be a consequence of their predominant cardiac chemosensory inputs, as well as their complex functional interconnectivity. Despite our limited understanding of the whole, current data indicate that the emergent properties displayed by most neurones comprising the cardiac neuroaxis will have to be taken into consideration when contemplating the targeting of its individual components if predictable, long-term therapeutic benefits are to accrue.
Localization of the Insulin-like Growth Factor II Binding Site to Amino Acids 1508–1566 in Repeat 11 of the Mannose 6-Phosphate/Insulin-like Growth Factor II Receptor (1995)

The mannose 6-phosphate/insulin-like growth factor II receptor (M6P/IGF-II receptor) binds insulin-like growth factor II (IGF-II) with high affinity. To localize the IGF-II binding site within the 15 repeating units that form the extracytoplasmic domain of the receptor, purified human M6P/IGF-II receptor was digested with thermolysin, and the fragments were analyzed for their ability to bind 125I-IGF-II in a cross-linking assay. Two IGF-II-binding receptor fragments of 23 and 37 kDa were purified. Sequence analysis revealed that the fragments consist of disulfide connected peptides comprising amino acids 1331-1566 and 1331-1697 of the receptor repeats 9-12. In a second approach we expressed truncated forms of the M6P/IGF-II receptor fused to the C terminus of the extracytoplasmic domain of the 46-kDa mannose 6-phosphate receptor. Fusion proteins containing M6P/IGF-II receptor repeats 10-15, 10-11, or 11-15 bound IGF-II, whereas a fusion protein containing the single repeat 10 failed to bind. This result indicates that repeat 11 (amino acids 1508-1650) is sufficient for binding of IGF-II. Residues 1508-1566, which are shared by the 23-kDa IGF-II-binding fragment and repeat 11, are proposed to form the IGF-II binding site of the M6P/IGF-II receptor.