gebhart/patrepeval huggingface dataset:
NMDA receptor antagonists: interactions with opioids (1997)

The N-methyl-D-aspartate (NMDA) receptor for glutamate has been implicated in the generation and maintenance of central (spinal) states of hypersensitivity. Thus antagonists at this receptor-channel complex have the potential not to totally abolish pain, but to prevent or block hyperalgesic states induced by tissue damage, inflammation, nerve damage and ischaemia. Information on amplification systems in the spinal cord such as the NMDA receptor is a step towards understanding why and how a painful stimulus is not always related to the response. There are now sufficient controlled clinical studies with agents such as ketamine to believe that, in humans, NMDA mediated events are critical in pathological and/or prolonged pain states. Consequently, use of antagonists may aid the treatment of difficult clinical pains when given alone or in combination with opioids. The combinations of opioids and NMDA antagonists may be especially helpful since some NMDA mediated events can be difficult to control with opioids alone (eg. neuropathic pain states). In addition, the ability of opioids to act presynaptically on C-fibre terminals to reduce transmitter release produces synergistic inhibitions with postsynaptically acting NMDA receptor antagonists. Consequently, low dose combinations may be possible with low side-effect liability. Finally, NMDA receptor activation would appear to be responsible for the generation of nitric oxide and prostanoids which further enhance pain transmission whereas adenosine release acts to control these NMDA mediated events. Thus, further targets for the indirect control of NMDA induced activity are possible.
Optimal handling of blood samples for routine measurement of lactate and pyruvate. (1994)

Blood lactate and pyruvate are of critical importance for the diagnosis of mitochondrial diseases. To determine guidelines for adequate blood pyruvate and lactate determinations, intraindividual studies were carried out on 10 subjects, and the influences of venostasis, delay before deproteinization, and pH in the pyruvate assay were analyzed. Delays of 1 hour or more before deproteinization of samples induced major elevations of lactate-pyruvate ratios. The lactate-pyruvate ratio correlated positively with pH in the pyruvate assay, and inadequate pH appeared as a largely underestimated cause of misleading results, while venostasis was a minor source of errors.
Influence of phospholipid asymmetry on fusion between large unilamellar vesicles (1992)

The ability of lipid asymmetry to regulate Ca(2+)-stimulated fusion between large unilamellar vesicles has been investigated. It is shown that for 100-nm-diameter LUVs composed of dioleoylphosphatidylcholine, dioleoylphosphatidylethanolamine, phosphatidylinositol, and dioleoylphosphatidic acid (DOPC/DOPE/PI/DOPA; 25:60:5:10) rapid and essentially complete fusion is observed by fluorescent resonance energy transfer techniques when Ca2+ (8 mM) is added. Alternatively, for LUVs with the same lipid composition but when DOPA was sequestered to the inner monolayer by incubation in the presence of a pH gradient (interior basic), little or no fusion is observed on addition of Ca2+. It is shown that the extent of Ca(2+)-induced fusion correlates with the amount of exterior DOPA. Further, it is shown that LUVs containing only 2.5 mol % DOPA, but where all the DOPA is in the outer monolayer, can be induced to fuse to the same extent and with the same rate as LUVs containing 5 mol % DOPA. These results strongly support a regulatory role for lipid asymmetry in membrane fusion and indicate that the fusogenic tendencies of lipid bilayers are largely determined by the properties of the monolayers proximate to the fusion interface.
The Pseudomonas putida peptidoglycan-associated outer membrane lipoprotein is involved in maintenance of the integrity of the cell cell envelope (1996)

Pseudomonas putida 14G-3, a derivative of the natural soil inhabitant P. putida KT2440, exhibited a chromosomal insertion of a mini-Tn5/'phoA transposon that resulted in reduced ability to colonize soil. In vitro characterization of P. putida 14G-3 revealed that it exhibited an altered cell morphology and envelope, as revealed by electron microscopy. The derived strain was sensitive to sodium dodecyl sulfate, deoxycholate, and EDTA, produced clumps when it reached high cell densities in the late logarithmic growth phase, and did not grow on low-osmolarity medium. The P. putida DNA surrounding the mini-Tn5/'phoA insertion was cloned and used as a probe to rescue the wild-type gene, which was sequenced. Comparison of the deduced peptide sequence with sequences in the Swiss-Prot database allowed the knocked-out gene to be identified as that encoding the peptidoglycan-associated lipoprotein (Pal or OprL) of P. putida. The protein was identified in coupled transcription and translation assays in vitro.
Techniques in plant molecular biology – progress and problems (1990)

Progress in plant molecular biology has been dependent on efficient methods of introducing foreign DNA into plant cells. Gene transfer into plant cells can be achieved by either direct uptake of DNA or the natural process of gene transfer carried out by the soil bacterium Agrobacterium. Versatile gene-transfer vectors have been developed for use with Agrobacterium and more recently vectors based on the genomes of plant viruses have become available. Using this technology the expression of foreign DNA, the functional analysis of plant DNA sequences, the investigation of the mechanism of viral DNA replication and cell to cell spread, as well as the study of transposition, can be carried out. In addition, the versatility of the gene-transfer vectors is such that they may be used to isolate genes not amenable to isolation using conventional protocols. This review concentrates on these aspects of plant molecular biology and discusses the limitations of the experimental systems that are currently available.
Device for the application of a dynamic biaxially uniform and isotropic strain to a flexible cell culture membrane (1994)

A large number of studies have demonstrated that mechanical perturbation modulates cellular metabolism; however, the systematic characterization of the molecular and cellular transduction mechanisms underlying mechanically induced metabolic modulation has been impeded, in part, by the limitations of the mechanical device. The objective of this investigation was to develop an in vitro experimental system that would provide independent control of the spatial and temporal biaxial strain distribution imposed on a flexible transparent tissue culture membrane that permits attachment, proliferation, and maintenance of the phenotypic expression of cultured embryonic osteoblasts. Such a device would permit a systematic investigation of the cellular response to specific, independently controlled parameters of mechanical deformation. Using a prototype device designed to impose a dynamic sinusoidal spatially isotropic biaxial strain profile, we confirmed experimentally that the strain was biaxially uniform and isotropic (radial = circumferential strain over the entire culture membrane) to within 14% (SD/mean) for the range of the peak strains tested (2.3-9.4%). Additionally, the uniformity was maintained at 1 Hz for at least 5 days of continuous operation. This experimental verification of the theoretically predicted isotropic strain profile suggests that the design principle is sound. Embryonic osteoblasts cultured on the flexible substrate proliferated and exhibited a temporal pattern of phenotypic expression (extracellular matrix accumulation and mineralization) comparable with that observed on polystyrene of tissue culture grade.
Safety and efficacy of repeat administration of samarium Sm‐153 lexidronam to patients with metastatic bone pain (2006)

Repeated dosing of 1.0 mCi/kg of Sm-153 was both safe and effective and is a reasonable treatment option in patients whose bone pain responds and then recurs after an initial dose provided that adequate hematologic function is present at the time of drug administration.
Quantitation of murine hematopoietic stem cells in vitro by limiting dilution analysis of cobblestone area formation on a clonal stromal cell line. (1993)

Murine hematopoietic stem cells with varying proliferative capacity can be assayed by limiting dilution analysis of "cobblestone area" (CA) formation on stromal layers in microlong-term bone marrow cultures. Cobblestone area forming cell (CAFC) frequency determined at early time points (day 7) correlates with mature stem cells measured as day 8 CFU-S, whereas CAFC frequency determined at day 28 correlates more closely with long-term marrow repopulating ability. Here we report a modification of the CAFC assay in which a clonal bone marrow stromal cell line, GB1/6, is substituted for fresh marrow-derived stromal layers. This modification simplifies the initial culture setup, eliminates inhomogeneities in the stromal layer and reduces the need for mice. Normal bone marrow CAFC frequencies were the same for both types of stromal cell underlayer, demonstrating the ability of a clonal cell line to completely replace the heterogeneous microenvironment of fresh stroma for in vitro stem cell support.
Role for the 3' end of the genome in determining disease specificity of Friend and Moloney murine leukemia viruses. (1983)

To probe the genetic basis of disease specificity of nondefective murine type C viruses, we are constructing recombinants in vitro between molecular clones of Friend murine leukemia virus (Fr-MuLV) and Moloney murine leukemia virus (Mo-MuLV). Fr-MuLV induces erythroleukemias when injected into newborn NFS mice, whereas Mo-MuLV almost invariably induces T-cell lymphomas. We find that a recombinant whose genome is derived primarily from Fr-MuLV but which has 621 nucleotides of Mo-MuLV information at its 3' end induces almost exclusively thymic lymphomas. The sequences derived from Mo-MuLV include 99 nucleotides encoding the carboxyl terminus of Prp15E, the origin of DNA +-strand synthesis, all of the U3 region, and 36 nucleotides of the R portion of the long terminal repeat. When the segment of Mo-MuLV was removed and replaced with the comparable segment from Fr-MuLV, the virus was again erythroblastosis-inducing. These results, in conjunction with studies from other laboratories [Laimins, L. A., Khoury, G., Gorman, C., Howard, B. & Gruss, P. (1982) Proc. Natl. Acad. Sci. USA 79, 6453-6457], suggest that transcriptional signals in U3 may determine tissue tropism and hence influence disease specificity ("targeting") of murine leukemia viruses.
Interaction of NPR1 with basic leucine zipper protein transcription factors that bind sequences required for salicylic acid induction of the PR-1 gene (1999)

The Arabidopsis thaliana NPR1 has been shown to be a key regulator of gene expression during the onset of a plant disease-resistance response known as systemic acquired resistance. The npr1 mutant plants fail to respond to systemic acquired resistance-inducing signals such as salicylic acid (SA), or express SA-induced pathogenesis-related (PR) genes. Using NPR1 as bait in a yeast two-hybrid screen, we identified a subclass of transcription factors in the basic leucine zipper protein family (AHBP-1b and TGA6) and showed that they interact specifically in yeast and in vitro with NPR1. Point mutations that abolish the NPR1 function in A. thaliana also impair the interactions between NPR1 and the transcription factors in the yeast two-hybrid assay. Furthermore, a gel mobility shift assay showed that the purified transcription factor protein, AHBP-1b, binds specifically to an SA-responsive promoter element of the A. thaliana PR-1 gene. These data suggest that NPR1 may regulate PR-1 gene expression by interacting with a subclass of basic leucine zipper protein transcription factors.
Human Major Histocompatibility Complex Contains Several Leukemia Susceptibility Genes (1994)

In mice, homozygosity for the Mhc haplotype H-2k is associated with increased susceptibility to spontaneous and virus-induced leukemia, lymphoma and other neoplasms in the predisposed host. The influence of the Mhc on malignant development in these models is to shorten the latency after virus inoculation. Here, we present evidence that a similar phenomenon results in early-onset of human leukemia. A molecular analysis of the MHC in 112 CML patients showed that those who developed the disease when aged less than 35 years (early-onset group) had higher homozygosity rates for the DOA1, HSP70 and C4 alleles of the DR53 group of ancestral haplotypes, for a subtype of HLA-A3, and a higher allele frequency of BfFb compared to the late-onset group. The oldest patient (n = 13) homozygous for DR53 was 52-years-old (p = 0.004), and all HLA-A3 homozygous patients (n = 4) were in the early-onset group (p = 0.01). The relative risk for early-onset CML yielded by HLA-A3 homozygosity was 17.6. The well-known serological HLA-Cw4 association was not confirmed at the DNA level and thought to be due to linkage disequilibrium with BfFb. The factor B association was sex-limited. The DR52 group haplotypes appeared to be protective. The HLA-identical sibling frequency was increased only in the early-onset group (p < 0.01). Our findings agree with the concept of an MHC influence on the development of malignancies. The similarity in the location of the susceptibility loci and the serological cross-reaction between H-2Ek and DR53 raise the possibility that the mouse and human MHC share the same leukemia susceptibility genes.
High flow rate microfluidic device for blood plasma separation using a range of temperatures (2009)

A hybrid microfluidic device that uses hydrodynamic forces to separate human plasma from blood cells has been designed and fabricated and the advantageous effects of temperature and flow rates are investigated in this paper. The blood separating device includes an inlet which is reduced by approximately 20 times to a small constrictor channel, which then opens out to a larger output channel with a small lateral channel for the collection of plasma. When tested the device separated plasma from whole blood using a wide range of flow rates, between 50 microl min(-1) and 200 microl min(-1), at the higher flow rates injected by hand and at temperatures ranging from 23 degrees C to 50 degrees C, the latter resulting in an increase in the cell-free layer of up to 250%. It was also tested continuously using between 5% and 40% erythrocytes in plasma and whole blood without blocking the channels or hemolysis of the cells. The mean percentage of plasma collected after separation was 3.47% from a sample of 1 ml. The percentage of cells removed from the plasma varied depending on the flow rate used, but at 37 degrees C ranged between 95.4 +/- 1% and 97.05 +/- 05% at 100 microl min(-1) and 200 microl min(-1), respectively. The change in temperature also had an effect on the number of cells removed from the plasma which was between 93.5 +/- 0.65% and 97.01 +/- 0.3% at 26.9 degrees C and 37 degrees C, respectively, using a flow rate of 100 microl min(-1). Due to its ability to operate in a wide range of conditions, it is envisaged that this device can be used in in vitro 'lab on a chip' applications, as well as a hand-held point of care (POC) device.
Characterization of vapor-phase-grown ZnSe nanoparticles (2002)

ZnSe nanoparticles were synthesized by reacting vapors of (CH3)2Zn:N(C2H5)3 and H2Se, diluted in H2, in an opposed flow reactor operating at room temperature and 120 Torr. The particles were collected as random aggregates on silicon substrates and transmission electron microscopy (TEM) grids placed downstream of the reaction zone. Particle characterization using TEM and electron diffraction revealed the presence of polycrystalline nanoparticles with diameter of about 40 nm that were apparently formed from coagulation of smaller nanocrystals with characteristic size of about 4 nm. Raman spectra of the nanoparticles revealed an asymmetrically broadened feature associated with the LO phonon of ZnSe, indicating the presence of smaller single-crystalline grains.
Multiple sclerosis in Iceland (1982)

Since 1974 we have attempted to ascertain all cases of MS beginning 1900-1975 in Iceland. As of October 1979 they numbered 168; all but 5 met all diagnostic criteria of the Schumacher Committee. Virtually all cases had been examined by a least one of the authors. Cases were few and sporadic from 1900 to 1922, then increased to a plateau for 1923-44, then again increased in 1945 with an irregular plateau thereafter. Average annual incidence rate for 1945-1954 was 3.2 per 100,000 population, significantly higher than the 1.6 for 1923-1944 or the 1.9 for 1955-1974. Age at onset was significantly decreased for cases with onset 1945-1949 and then sharply increased for those with 1950-1954 onsets. The occurrence of MS in 1945-1954 meets the criteria for a point-source epidemic, whose tail thereafter mérged into what may be "baseline" for Iceland. This postwar epidemic is then similar to that recently described for the Faroe Islands, a land that shares its history, culture, and peoples with Iceland.
Doubly Randomized Delayed-Start Design for Enrichment Studies with Responders or Nonresponders (2012)

High placebo response has been a major source of bias and is difficult to deal with in many central nervous system (CNS) clinical trials. This bias has led to a high failure rate in mood disorder trials even with known effective drugs. For cancer trials, the traditional parallel group design biases the inference on the maintenance effect of the new drug with the traditional time-to-treatment failure analysis. To minimize bias, we propose a doubly randomized delayed-start design for clinical trials with enrichment. The design consists of two periods. In the first period, patients can be randomized to receive several doses of a new drug or a control. In the second period, control patients of the first period of an enriched population can be rerandomized to receive the same or fewer doses of the new drug or to continue on the control. Depending on the clinical needs, different randomization ratios can be applied to the two periods. The essential feature is that the design is naturally adaptive because of the randomization for the second period. As a result, other aspects of the second period, such as the sample size, can be modified adaptively when an interim analysis is set up for the first period. At the end of the trial, response data from both randomizations are combined in an integrated analysis. Because of the enrichment in the second period, the design increases the probability of trial success and, in addition, reduces the required sample size. Thus, for clinical development, the design offers greater efficiency.
Comparative Evaluation of Three Lignin Isolation Protocols for Various Wood Species (2006)

Milled wood lignin (MWL), cellulolytic enzyme lignin (CEL), and enzymatic mild acidolysis lignin (EMAL) were isolated from different wood species and characterized by various techniques. The EMAL protocol offered gravimetric lignin yields 2-5 times greater than those of the corresponding MWL and CEL. The purities of the EMALs were 3.75-10.6% higher than those of their corresponding CELs, depending upon the wood species from which they were isolated. Molecular weight analyses showed that the EMAL protocol isolates lignin fractions that are not accessed by the other procedures evaluated, while 31P NMR spectroscopy revealed that MWL is more condensed and bears more phenolic hydroxyl groups than EMAL and CEL. The yields and purities of EMAL, MWL, and CEL from hardwood were greater than those obtained for the examined softwoods. Structural details obtained by DFRC (derivatization followed by reductive cleavage)/31P NMR revealed different contents of condensed and uncondensed beta-O-aryl ether structures, dibenzodioxocins, and condensed and uncondensed phenolic hydroxyl and carboxylic acid groups within lignins isolated from different wood species.
Crystal Structure of Mycobacterium tuberculosis Diaminopimelate Decarboxylase, an Essential Enzyme in Bacterial Lysine Biosynthesis (2003)

The Mycobacterium tuberculosis lysA gene encodes the enzyme meso-diaminopimelate decarboxylase (DAPDC), a pyridoxal-5'-phosphate (PLP)-dependent enzyme. The enzyme catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. The lysA gene of M. tuberculosis H37Rv has been established as essential for bacterial survival in immunocompromised mice, demonstrating that de novo biosynthesis of lysine is essential for in vivo viability. Drugs targeted against DAPDC could be efficient anti-tuberculosis drugs, and the three-dimensional structure of DAPDC from M. tuberculosis complexed with reaction product lysine and the ternary complex with PLP and lysine in the active site has been determined. The first structure of a DAPDC confirms its classification as a fold type III PLP-dependent enzyme. The structure shows a stable 2-fold dimer in head-to-tail arrangement of a triose-phosphate isomerase (TIM) barrel-like alpha/beta domain and a C-terminal beta sheet domain, similar to the ornithine decarboxylase (ODC) fold family. PLP is covalently bound via an internal aldimine, and residues from both domains and both subunits contribute to the binding pocket. Comparison of the structure with eukaryotic ODCs, in particular with a di-fluoromethyl ornithine (DMFO)-bound ODC from Trypanosoma bruceii, indicates that corresponding DAP-analogues might be potential inhibitors for mycobacterial DAPDCs.
Isolation and functional expression in Escherichia coli of a gene encoding phosphatidylethanolamine methyltransferase (EC 2.1.1.17) from Rhodobacter sphaeroides (1993)

Phosphatidylcholine is a major component of membranes in most eukaryotes, but it is found only in a small number of bacteria, where it is synthesized by N-methylation of phosphatidylethanolamine. In yeast and other fungi the methylation of phosphatidylethanolamine to phosphatidylcholine proceeds in two steps: the methylation of phosphatidylethanolamine by phosphatidylethanolamine methyltransferase followed by the methylation of monomethylphosphatidylethanolamine by phospholipid methyltransferase. Here we describe the isolation of two allelic phosphatidylcholine-deficient mutants of Rhodobacter sphaeroides which are unable to methylate phosphatidylethanolamine, monomethylphosphatidylethanolamine, or dimethylphosphatidylethanolamine. A DNA fragment containing a gene designated pmtA, which encodes a 22.9-kDa protein, was found to complement both mutants. Expression of this gene in Escherichia coli, which normally lacks phosphatidylcholine or methylated derivatives of phosphatidylethanolamine, resulted in the formation of phosphatidylcholine. A protein extract derived from the E. coli strain expressing the pmtA gene was able to convert phosphatidylethanolamine, mono- and dimethylphosphatidylethanolamine into phosphatidylcholine. Based on these data we conclude that the product of the pmtA gene catalyzes a sequence of three chemically distinct, methylation reactions beginning with phosphatidylethanolamine and leading to the formation of phosphatidylcholine in R. sphaeroides.