gebhart/patrepeval huggingface dataset:
An antibody VH domain with a lox‐Cre site integrated into its coding region: bacterial recombination within a single polypeptide chain (1995)

Bacterial lox-Cre recombination within a single antibody VH domain was achieved through integration of a loxP site into its coding sequence. The 5' half of the VH gene, in which the H2 loop was replaced by a mutant loxP site, was fused to geneIII in an 'acceptor' fd-phage vector containing also a wild type loxP site. With a 'donor' plasmid vector harbouring the 3' half of the VH gene flanked by the same, differing loxP sites it recombined into a full-length VH with the loxP site-H2 loop. This VH was purified from bacterial periplasm, where it folded into a typical immunoglobulin domain. The system allows the generation of large VH repertoires using lox-Cre recombination.
Nuclear posttranscriptional processing of thymidine kinase mRNA at the onset of DNA synthesis. (1988)

The posttranscriptional regulatory mechanism(s) underlying thymidine kinase (TK) mRNA accumulation was investigated in BALB/c 3T3 cells during their progression from G0 into S phase of the cell cycle. Very little TK mRNA could be detected in either the nuclear or the cytoplasmic compartment from cells harvested in G0 or G1. At the onset of S phase, however, the level of nuclear TK mRNA precursors and mature TK mRNAs increased dramatically. The high molecular weight TK heterogeneous nuclear RNA species detected in the nuclei of S-phase cells were polyadenylylated and hybridized to intron sequences derived from the TK gene. A series of high molecular weight precursors could be chased to lower molecular weight species in the presence of actinomycin D, suggesting an ordered removal of intron sequences with the kinetics of a precursor-product relationship. These results demonstrate a striking change in the nuclear posttranscriptional processing of TK heterogeneous nuclear RNA at the G1-S boundary and, furthermore, define a model system for the examination of RNA-processing events in vivo.
Optoelectronic tweezers integration with multilayer microfluidic device using SWNT embeded PDMS membrane electrode (2011)

We report an optoelectronic tweezers (OET) integrated with a multiplayer PDMS based microfluidic device via a flexible single-walled carbon nanotube (SWNT) embedded thin film membrane. It realizes the first microfluidic integrated OET with on chip valve and pump functions.
Flip-chip approach to endfire coupling between single-mode optical fibres and channel waveguides (1976)

We report a practical approach to the positioning of a number of single-mode fibres for endfire coupling to channel waveguides. Boivin&apos;s approach has been extended to a flip-chip configuration which permits its use with substrates other than silicon.
Human Pharmacokinetics of Intravenous, Sublingual, and Buccal Buprenorphine (1996)

Buprenorphine is a potent opioid analgesic used in the treatment of moderate to severe pain. At higher doses, it has demonstrated potential for treating heroin dependence. This study was undertaken to investigate buprenorphine pharmacokinetics by different routes of administration at dosages approximating those used in opioid-dependence studies. Six healthy men who were nondependent but who had a history of heroin use were administered buprenorphine in a crossover design study by intravenous (1.2 rag), sublingual (4.0 rag), and buccal (4.0 rag) routes of administration. Plasma samples were collected up to 96 h and assayed for buprenorphine and norbuprenorphine by negative chemical ionization tandem mass spectrometry. Plasma concentrations of buprenorphine and norbuprenorphine were analyzed by nonlinear regression analysis with standard noncompartmental methods. Buprenorphine bioavailability by the sublingual and buccal routes was estimated as 51.4% and 27.8%, respectively, although there was considerable interindividual variability by both routes of administration. The terminal elimination half-lives were longer for the sublingual and buccal routes than for the intravenous route. The extended elimination half-lives may be due to a shallow depot effect involving sequestration of buprenorphine in the oral mucosa. Norbuprenorphine mean peak plasma concentrations were less than 1 ng/mL and were highly variable among different routes of administration and individuals. The terminal elimination half-life of norbuprenorphine was longer than buprenorphine.
Hemoprotein H-450 Identified as a Form of Cytochrome P-450 Having an Endogenous Ligand at the 6th Coordination Position of the Heme (1984)

Hemoprotein H-450 was purified from rat liver cytosol to homogeneity by an improved procedure. The purified H-450 showed a subunit molecular weight of 64,000 daltons and contained 0.7-0.9 mol of protoheme per mol subunit. Among rat tissues examined, liver and kidney contained significant amounts of H-450 in the cytosol. Oxidized H-450 showed a Soret peak at 428 nm and a broad beta band at around 550 nm. Reduced H-450 was found to exist in two interconvertible forms, alkaline and acid forms. The alkaline form showed Soret, beta, and alpha peaks at 448, 540, and 571 nm, whereas the acid form showed Soret, beta, and alpha peaks at 425, 530, and 558 nm. The spectral properties of both oxidized and reduced H-450 in alkaline medium resemble those of cytochrome P-450 having a nitrogenous ligand at the 6th coordination position of the heme. Upon addition of low concentrations of HgCl2, H-450 was converted to a denatured form both in the oxidized and the reduced states and lost its unique spectral characteristics. Addition of carbon monoxide to reduced H-450 produced a new spectral species which resembled that of the reduced carbon monoxide complex of P-420, a denatured form of cytochrome P-450. Comparison of the EPR signal of oxidized H-450 with those of a cytochrome P-450, P-450(PB-1), and several model compounds indicated the presence of a thiolate anion at the 5th coordination position of the heme of H-450. Judging from EPR data, oxidized H-450 also converts between acid and alkaline forms, whose signals were observed at g = 1.867, 2.31, and 2.507 and at g = 1.910, 2.28, and 2.424, respectively. These lines of evidence indicate that the 5th and 6th coordination positions of the heme of H-450 are a thiolate and a nitrogenous group, respectively. With respect to the heme environments, H-450 is a member of the cytochrome P-450 family, and has a nitrogenous ligand at the 6th coordination position of the heme.
An Approach for Automatic Pain Detection through Facial Expression (2016)

Automatic pain detection is an emerging area of investigation with convenient applications in health care. The variation in facial expression often provides a clue for occurrence of pain. It provides an important window for the person who cannot verbally describe or rate their level of pain. To meet up the specific necessities, a framework has been designed for extraction of features from the face for automatic pain detection through facial expression. In this framework, Gabor filtering and Principal Component Analysis (PCA) are used as contributive steps that improves the performance of the system in terms of accuracy. To verify the accuracy and robustness of the system, experiments have been conducted on UNBC-McMaster Shoulder Pain Expression Archive Database at both frame level (person dependent) and image level (person independent). The methodology achieves 87.23% accuracy for detection of pain at frame level. Also the methodology achieves 82.43% accuracy for classifying the frames between four pain level (i.e. PSPI of 0, 1, 2 and >=3). The success rate of the methodology for pain detection at image level is 95.5%.
Percutaneous Coronary Intervention at Centers With and Without On-Site Surgical Backup (2015)

Clinical outcomes and complication rates of PCI at centers without on-site surgery did not differ from those with on-site surgery, for both primary and nonprimary PCI. Temporal trends indicated improving clinical outcomes in nonprimary PCI at centers without on-site surgery.
Safety and efficacy of loteprednol etabonate ophthalmic ointment 0.5% for the treatment of inflammation and pain following cataract surgery (2011)

LE ointment was efficacious and well tolerated in the treatment of ocular inflammation and pain following cataract surgery.
Synthesis of polymers containing pseudohalide groups by cationic polymerization 4. Cocatalysis as a direct route to end‐capped poly(2‐methylpropene) with pseudohalide groups (1992)

Abstract The possibility to functionalize poly(2‐methylpropene) (PIB) by direct synthesis with functions containing nitrogen derived from the group of pseudohalogens, is demonstrated. Polymerization by cationic polyaddition of 2‐methylpropene using a suitable cocatalyst, here hydrazoic acid HN 3 or hydrocyanic acid HCN, in the presence of titanium tetrachloride is carried out in methylene dichloride. The highest functionalization efficiency ( f = 0,7) is obtained for a mole ratio catalyst‐to‐cocatalyst close to one. Part of the macromolecules is found to contain twice as many tert ‐butyl groups as internal unsaturations. This finding is explained by the occurrence of some dimerization of macromonomers, which are formed by a PIB backbone terminated by one disubstituted unsaturation.
Shelf life enhancement of plant growth promoting rhizobacteria using a simple formulation screening method (2018)

Plant growth promoting rhizobacteria (PGPR) are a specific group of bacteria interacting beneficially with plants. Among the known PGPRs, the species Pseudomonas fluorescens and Burkholderia pyrrocinia have been highlighted in both growth promotion and control of rice diseases. Ensuring the stability of the microorganism during production, formulation, distribution and storage has been a challenge for these species. In this context, the objective of this work was to develop liquid formulations, through a simplified process, that allows increase in the shelf life of these rhizobacteria for commercial application. Both bacteria were tested in 32 formulations under two storage temperature conditions: 8 and 28&deg;C, resulting in 64 treatments for each species, which were evaluated for 180 days. Combinations of the adjuvants: molasses, glycerol, NaCl, PVP, MgSO4, K2HPO4 and yeast extract were evaluated. Formulations containing molasses, stored at 8&deg;C, were considered the most efficient in maintaining microbial viability. The method used was considered efficient to select three formulations that allowed maintenance of the concentration of viable cells of P. fluorescens and B. pyrrocinia in 108 cfu.mL-1, for at least 90 and 150 days, respectively, not interfering with bacterial action potential. &nbsp; Key words: Pseudomonas fluorescens, Burkholderia pyrrocinia, plant growth promoting rhizobacteria, shelf life, liquid formulations. &nbsp;
Effects of liquid stimuli on dual-axis swallowing accelerometry signals in a healthy population (2010)

We conclude that stimulus type does affect specific characteristics of dual-axis swallowing accelerometry signals, suggesting that associated clinical screening protocols may need to be stimulus specific.
The pharmacology and mechanism of action of riluzole (1996)

The excitotoxic hypothesis of neurodegeneration has stimulated much interest in the possibility of using compounds that will block excitotoxic processes to treat neurologic disorders. Riluzole is a neuroprotective drug that blocks glutamatergic neurotransmission in the CNS. Riluzole inhibits the release of glutamic acid from cultured neurons, from brain slices, and from corticostriatal neurons in vivo. It is thought these effects may be partly due to inactivation of voltage-dependent sodium channels on glutamatergic nerve terminals, as well as activation of a G-protein-dependent signal transduction process. Riluzole also blocks some of the postsynaptic effects of glutamic acid by noncompetitive blockade of N-methyl-D-aspartate (NMDA) receptors. In vivo, riluzole has neuroprotective, anticonvulsant, and sedative properties. In a rodent model of transient global cerebral ischemia, a complete suppression of the ischemia-evoked surge in glutamic acid release has been observed. In vitro, riluzole protects cultured neurons from anoxic damage, from the toxic effects of glutamic-acid-uptake inhibitors, and from the toxic factor in the CSF of patients with amyotrophic lateral sclerosis.
Triggering the Interferon Antiviral Response Through an IKK-Related Pathway (2003)

Rapid induction of type I interferon expression, a central event in establishing the innate antiviral response, requires cooperative activation of numerous transcription factors. Although signaling pathways that activate the transcription factors nuclear factor kappaB and ATF-2/c-Jun have been well characterized, activation of the interferon regulatory factors IRF-3 and IRF-7 has remained a critical missing link in understanding interferon signaling. We report here that the IkappaB kinase (IKK)-related kinases IKKepsilon and TANK-binding kinase 1 are components of the virus-activated kinase that phosphorylate IRF-3 and IRF-7. These studies illustrate an essential role for an IKK-related kinase pathway in triggering the host antiviral response to viral infection.
Spontaneous Tumor-Specific Humoral and Cellular Immune Responses to NY-ESO-1 in Hepatocellular Carcinoma (2004)

This is the first report of a spontaneous immune response in HCC patients to a known tumor-specific antigen, NY-ESO-1 protein. Our data favor the possibility of immunotherapeutic strategies for the treatment of HCC.
Cybernetic Modeling and Regulation of Metabolic Pathways in Multiple Steady States of Hybridoma Cells (2000)

Hybridoma cells utilize a pair of complementary and partially substitutable substrates, glucose and glutamine, for growth. It has been shown that cellular metabolism shifts under different culture conditions. When those cultures at different metabolic states are switched to a continuous mode, they reach different steady states under the same operating conditions. A cybernetic model was constructed to describe the complementary and partial substitutable nature of substrate utilization. The model successfully predicted the metabolic shift and multiple steady-state behavior. The results are consistent with the experimental observation that the history of the culture affects the resulting steady state.
New Hydrolysis-Dependent Thermosensitive Polymer for an Injectable Degradable System (2007)

Novel, bioerodible, thermosensitive poly(NIPAAm-co-dimethyl-gamma-butyrolactone acrylate), with a hydrolysis-dependent thermosensitivity, was synthesized by radical polymerization with a varying dimethyl-gamma-butyrolactone acrylate (DBA) content, and the properties of the copolymers were characterized using differential scanning calorimetry, gel permeation chromatography in conjunction with static light scattering, Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR), and acid titration. The lower critical solution temperature of the copolymers decreases with increasing DBA content, but then increases after ring-opening hydrolysis of the DBA side group. FTIR and NMR spectra showed the copolymerization of these two monomers and the hydrolysis-dependent ring-opening of the DBA side group. It was also found that there are no low-molecular-weight byproducts but rather dissolution of the polymer chains at 37 degrees C during the time frame of application. Models of the kinetics suggest that the hydrolysis reaction is self-catalytic due to an increase in hydrophilicity and charge, and thus accessible water concentration, caused by ring-opening of the DBA.
Queueing disciplines for integrated fast packet networks (2003)

The authors focus on the problem of internodal link queueing in integrated fast packet networks. The queueing discipline used to multiplex packets onto an internodal link is an important element in the overall bandwidth management of an integrated fast packet network. The characteristics of and quality of service required by different traffic classes are reviewed and used as the basis for comparing alternative queueing disciplines. A hybrid weighted round-robin and head-of-line priority discipline are shown to provide appropriate allocation of the internodal link bandwidth among different traffic classes, while allowing decay differentiation within a traffic class.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Orthogonal Cas9–Cas9 chimeras provide a versatile platform for genome editing (2018)

The development of robust, versatile and accurate toolsets is critical to facilitate therapeutic genome editing applications. Here we establish RNA-programmable Cas9-Cas9 chimeras, in single- and dual-nuclease formats, as versatile genome engineering systems. In both of these formats, Cas9-Cas9 fusions display an expanded targeting repertoire and achieve highly specific genome editing. Dual-nuclease Cas9-Cas9 chimeras have distinct advantages over monomeric Cas9s including higher target site activity and the generation of predictable precise deletion products between their target sites. At a therapeutically relevant site within the BCL11A erythroid enhancer, Cas9-Cas9 nucleases produced precise deletions that comprised up to 97% of all sequence alterations. Thus Cas9-Cas9 chimeras represent an important tool that could be particularly valuable for therapeutic genome editing applications where a precise cleavage position and defined sequence end products are desirable.
Hepatitis B Virus (HBV) Surface Antigen Interacts with and Promotes Cyclophilin A Secretion: Possible Link to Pathogenesis of HBV Infection (2010)

Cyclophilin A (CypA), predominantly located intracellularly, is a multifunctional protein. We previously reported decreased CypA levels in hepatocytes of transgenic mice expressing hepatitis B virus (HBV) surface antigen (HBsAg). In this study, we found that expression of HBV small surface protein (SHBs) in human hepatoma cell lines specifically triggered CypA secretion, whereas SHBs added extracellularly to culture medium did not. Moreover, CypA secretion was not promoted by the expression of a secretion deficient SHBs mutant, suggesting a close association between secretion of CypA and SHBs. Interaction between CypA and SHBs was observed by using coimmunoprecipitation and glutathione S-transferase pull-down assays. Hydrodynamic injection of the SHBs expression construct into C57BL/6J mice resulted in increased serum CypA levels and ALT/AST levels, as well as the infiltration of inflammatory cells surrounding SHBs-positive hepatocytes. The inflammatory response and serum ALT/AST level were reduced when the chemotactic effect of CypA was inhibited by cyclosporine and anti-CD147 antibody. Furthermore, higher serum CypA levels were detected in chronic hepatitis B patients than in healthy individuals. In HBV patients who had received liver transplantation, serum CypA levels declined dramatically after the loss of HBsAg as a consequence of liver transplantation. Taken together, these results indicate that expression and secretion of SHBs can promote CypA secretion, which may contribute to the pathogenesis of HBV infection.
Catch Bonds in Adhesion (2008)

One of the most exciting discoveries in biological adhesion is the recent and counter-intuitive observation that the lifetimes of some biological adhesive bonds, called catch bonds, are enhanced by tensile mechanical force. At least two types of adhesive proteins have been shown to form catch bonds--blood proteins called selectins and a bacterial protein called FimH. Both mediate shear-enhanced adhesion, in which cells bind more strongly at high shear than at low shear. Single-molecule experiments and cell-free assays have now clearly demonstrated that catch bonds exist and mediate shear-enhanced adhesion. However, the mechanics of cellular organelles also contribute to shear-enhanced adhesion by modulating the force applied to catch bonds. This review examines how individual catch bond behavior contributes to shear-enhanced cellular adhesion for the two best-understood examples. The lessons from these systems offer design principles for understanding other types of shear-enhanced adhesion and for engineering nanostructured force-dependent adhesives out of catch bonds.
Ras Signaling Is Required for Serum-Induced Hyphal Differentiation in Candida albicans (1999)

Serum induces Candida albicans to make a rapid morphological change from the yeast cell form to hyphae. Contrary to the previous reports, we found that serum albumin does not play a critical role in this morphological change. Instead, a filtrate (molecular mass, <1 kDa) devoid of serum albumin induces hyphae. To study genes controlling this response, we have isolated the RAS1 gene from C. albicans by complementation. The Candida Ras1 protein, like Ras1 and Ras2 of Saccharomyces cerevisiae, has a long C-terminal extension. Although RAS1 appears to be the only RAS gene present in the C. albicans genome, strains homozygous for a deletion of RAS1 (ras1-2/ras1-3) are viable. The Candida ras1-2/ras1-3 mutant fails to form germ tubes and hyphae in response to serum or to a serum filtrate but does form pseudohyphae. Moreover, strains expressing the dominant active RAS1(V13) allele manifest enhanced hyphal growth, whereas those expressing a dominant negative RAS1(A16) allele show reduced hyphal growth. These data show that low-molecular-weight molecules in serum induce hyphal differentiation in C. albicans through a Ras-mediated signal transduction pathway.
Approach to Validating an Opsonophagocytic Assay for Streptococcus pneumoniae (2005)

Streptococcus pneumoniae (pneumococcus) polysaccharide serotype-specific antibodies that have opsonophagocytic activity are considered a primary mechanism of host defense against pneumococcal disease. In vitro opsonophagocytic assays (OPAs) with antibody and complement to mediate opsonophagocytic killing of bacteria have been designed and developed as an adjunct to the standardized serum immunoglobulin G antipneumococcal capsular polysaccharide enzyme immunoassay to assess the effectiveness of pneumococcal vaccines. OPA presents challenges for assay standardization and assay precision due to the multiple biologically active and labile components involved in the assay, including human polymorphonuclear leukocytes or cultured effector cells, bacteria, and complement. Control of these biologically labile components is critical for consistent assay performance. An approach to validating the performance of the assay in accordance with International Conference for Harmonization guidelines, including its specificity, intermediate precision, accuracy, linearity, and robustness, is presented. Furthermore, we established parameters for universal reagents and standardization of the use of these reagents to ensure the interlaboratory reproducibility and validation of new methodologies.
Radiation Pressure on a Small Rigid Sphere (1967)

Simple expressions are derived for the acoustic radiation force F on a small rigid sphere of radius a, volume v and density ρ suspended In a liquid or gas of density ρ0. Effects of viscosity are neglected; use is made of methods developed by King and Embleton. Results are expressed in terms of the time-averaged densities T̄a and V̄a of kinetic and potential energies, respectively, in the incident sound field. Letting β be ρ0/ρ it is found. as an approximation when a is much less than the sonic wavelength, that F = v[B∇T̄a − ∇V̄a]+Δ, B − 3 1 − β /(2+β), where Δ is given by a relatively complicated expression. The quantity Δ is important primarily in progressive waves of relatively uniform amplitude, as exist in the field of a large source; here ∇T̄a and ∇V̄a, may be relatively small while gradients of the phase exist. In a standing wave or in the neighborhood of a small source, Δ is negligible. When Δ = 0, the above expression for F agrees with one given previously by Gor'kov.