gebhart/patrepeval huggingface dataset:
Investigation of some properties of oligodeoxynucleotides containing 4'- thio-2'-deoxynucleotides: duplex hybridization and nuclease sensitivity (1996)

The thermal stabilities of the duplexes formed between 4'-thio-modified oligodeoxynucleotides and their DNA and RNA complementary strands were determined and compared with those of the corresponding unmodified oligodeoxynucleotides. A 16mer oligodeoxynucleotide containing 10 contiguous 4'-thiothymidylate modifications formed a less stable duplex with the DNA target (deltaTm/modification -1.0 degrees C) than the corresponding unmodified oligodeoxynucleotide. However, when the same oligodeoxynucleotide was bound to the corresponding RNA target, a small increase in Tm was observed (deltaTm/modification +0.16 degrees C) when compared with the unmodified duplex. A study to identify the specificity of an oligodeoxynucleotide containing a 4'-thiothymidylate modification when forming a duplex with DNA or RNA containing a single mismatch opposite the modification found the resulting Tms to be almost identical to the wild-type duplexes, demonstrating that the 4'-thio-modification in oligodeoxynucleotides has no deleterious effect on specificity. The nuclease stability of 4'-thio-modified oligodeoxynucleotides was examined using snake venom phosphodiesterase (SVPD) and nuclease S1. No significant resistance to degradation by the exonuclease SVPD was observed when compared with the corresponding unmodified oligodeoxynucleotide. However, 4'-thio-modified oligodeoxynucleotides were found to be highly resistant to degradation by the endonuclease S1. It was also demonstrated that 4'-thio-modified oligodeoxynucleotides elicit Escherichia coli RNase H hydrolysis of the RNA target only at high enzyme concentration.
A single base pair change in proline biosynthesis genes causes osmotic stress tolerance (1988)

A single base pair change has been found in a site corresponding to a regulatory region of the first enzyme in the proline biosynthetic pathway. This change alters feedback inhibition and is responsible for the synthesis of high levels of proline that enable Escherichia coli to withstand osmotic stress.
Direct transesterification of all classes of lipids in a one-step reaction. (1986)

Conventional techniques for the determination of fatty acid composition of lipids require solvent extraction, purification, hydrolysis, and derivatization procedures that are both lengthy and cumbersome. A 1-hr direct transesterification procedure carried out in methanol-benzene 4:1 with acetyl chloride circumvented all these steps and was applicable for analysis of both simple (triglycerides) and complex lipids (cholesteryl esters, phospholipids, and sphingomyelin). Recoveries (greater than 95%) of standards unaffected by the presence of 5% water and 200 mg of silica suggested that the technique could be used for the quantitative analysis of total fatty acids as well as of fatty acids in classes of lipids separated on silica from biological samples. When compared to the Folch procedure, the technique led to a 20.1% increase in total fatty acids for plasma, 3.9% for feces, 7.4% for bile, and 9.7% for rat liver. We therefore conclude that this one-step direct transesterification procedure is superior to currently used methods, not only because of its simplicity and speed, but also because of its added precision.
Chlamydomonas reinhardtii Tubulin Gene Structure (1986)

DNA sequencing studies have provided a picture of the total information available at the gene level for tubulin production in C. reinhardtii. The data indicates that diversity at the gene level is very limited and that all the microtubules in the cell are composed of a very similar set of tubulins. These studies contrast with similar studies of S. pombe alpha-tubulin genes and chicken beta-tubulin genes that show much heterogeneity among members of the same gene family. Further studies will be needed to investigate whether the high degree of conservation of tubulin genes is unique or common among lower eukaryotes, and what mechanisms are used to maintain homogeneity in C. reinhardtii tubulin gene families. Our DNA sequence analysis, in addition to the work of Brunke et al., has provided information on the noncoding, and possibly regulatory, portions of the tubulin genes. For example, the promoter regions of the 4 tubulin genes share a consensus sequence of 16 nucleotides upstream of the TATA box. This sequence could be involved in regulating the coordinate expression of the genes. Although little homology exists generally in the noncoding region of the genes, striking homology between the third IVS in each beta-tubulin gene is observed. Small elements homologous to the beta-tubulin IVS 3 also exist in the second IVS of each alpha-tubulin gene. In addition, considerable homology in the 5' noncoding portion of the alpha-tubulin transcripts has been noted. These homologies may be the result of recent gene conversion events, and may not have functional significance. The possibility, however, must also be considered in future experiments that these elements may play a role in regulating the expression of the tubulin genes.
Dimerization of Human Growth Hormone by Zinc (1991)

Size-exclusion chromatography and sedimentation equilbrium studies demonstrated that zinc ion (Zn2+) induced the dimerization of human growth hormone (hGH). Scatchard analysis of 65Zn2+ binding to hGH showed that two Zn2+ ions associate per dimer of hGH in a cooperative fashion. Cobalt (II) can substitute for Zn2+ in the hormone dimer and gives a visible spectrum characteristic of cobalt coordinated in a tetrahedral fashion by oxygen- and nitrogen-containing ligands. Replacement of potential Zn2+ ligands (His18, His21, and Glu174) in hGH with alanine weakened both Zn2+ binding and hGH dimer formation. The Zn(2+)-hGH dimer was more stable than monomeric hGH to denaturation in guanidine-HCl. Formation of a Zn(2+)-hGH dimeric complex may be important for storage of hGH in secretory granules.
A new species of the genusdimorphostylis(cumacea, diastylidae) from Korea (2002)

A new species, Dimorphostylis namhaedoensis (Cumacea, Diastylidae) is described on the basis of the specimens collected from southern shallow coast of Korean peninsula. The new species resembles four other species, D. asiatica, D. valida, D. hisuta and D. acroplicata, in having three apical spines on the terminal margin of the male telson and three pairs of the oblique ridges on the carapace, but are obviously distinguished from them in that the pattern of the ridges on the carapace is different and the third article of the antennular peduncle is very long in female. Furthermore, the dorsal carina of the female carapace has a row of forward spines and among the three apical spines of male telson, the median spine is much smaller than the lateral ones.
Identification of Human Proteins Functionally Conserved with the Yeast Putative Adaptors ADA2 and GCN5 (1996)

Transcriptional adaptor proteins are required for full function of higher eukaryotic acidic activators in the yeast Saccharomyces cerevisiae, suggesting that this pathway of activation is evolutionarily conserved. Consistent with this view, we have identified possible human homologs of yeast ADA2 (yADA2) and yeast GCN5 (yGCN5), components of a putative adaptor complex. While there is overall sequence similarity between the yeast and human proteins, perhaps more significant is conservation of key sequence features with other known adaptors. We show several functional similarities between the human and yeast adaptors. First, as shown for yADA2 and yGCN5, human ADA2 (hADA2) and human GCN5 (hGCN5) interacted in vivo in a yeast two-hybrid assay. Moreover, hGCN5 interacted with yADA2 in this assay, suggesting that the human proteins form similar complexes. Second, both yADA2 and hADA2 contain cryptic activation domains. Third, hGCN5 and yGCN5 had similar stabilizing effects on yADA2 in vivo. Furthermore, the region of yADA2 that interacted with yGCN5 mapped to the amino terminus of yADA2, which is highly conserved in hADA2. Most striking, is the behavior of the human proteins in human cells. First, GAL4-hADA2 activated transcription in HeLa cells, and second, either hADA2 or hGCN5 augmented GAL4-VP16 activation. These data indicated that the human proteins correspond to functional homologs of the yeast adaptors, suggesting that these cofactors play a key role in transcriptional activation.
Pulsed-laser atom-probe field-ion microscopy (1980)

A time-of-flight atom-probe field-ion microscope has been developed which uses nanosecond laser pulses to field evaporate surface species. The ability to operate an atom-probe without using high-voltage pulses is advantageous for several reasons. The spread in energy arising from the desorption of surface species prior to the voltage pulse attaining its maximum amplitude is eliminated, resulting in increased mass resolution. Semiconductor and insulator samples, for which the electrical resistivity is too high to transmit a short-duration voltage pulse, can be examined using pulsed-laser assisted field desorption. Since the electric field at the surface can be significantly smaller, the dissociation of molecular adsorbates by the field can be reduced or eliminated, permitting well-defined studies of surface chemical reactions. In addition to atom-probe operation, pulsed-laser heating of field emitters can be used to study surface diffusion of adatoms and vacancies over a wide range of temperatures. Examples demonstrating each of these advantages are presented, including the first pulsed-laser atom-probe (PLAP) mass spectra for both metals (W, Mo, Rh) and semiconductors (Si). Molecular hydrogen, which desorbs exclusively as atomic hydrogen in the conventional atom probe, is shown to desorb undissociatively in the PLAP. Field-ion microscope observations of the diffusion and dissociation of atomic clusters, the migration of adatoms, and the formation of vacancies resulting from heating with a 7-ns laser pulse are also presented.
An Investigation of Changes in Physical Properties of Injectable Calcium Hydroxylapatite in a Carrier Gel When Mixed with Lidocaine and with Lidocaine/Epinephrine (2008)

INTRODUCTION As physicians incorporate calcium hydroxylapatite (CaHA) into their aesthetic treatment regimens, the question has arisen of whether the addition of anesthetic agents to prefilled CaHA syringes might provide sufficient anesthetic prophylaxis to warrant reduction in conventional anesthetic pretreatment procedures. STUDY DESIGN Investigators sought to determine changes in the physical properties of CaHA induced by the addition of lidocaine and lidocaine with epinephrine into the prefilled CaHA syringe. The CaHA and gel carrier (CHM) were mixed with varying amounts of lidocaine and lidocaine with epinephrine to measure the number of passes back and forth for optimal homogeneity of lidocaine and CaHA in syringes, changes in viscosity, extrusion force, needle jam rates, elasticity, and pH. RESULTS Ten mixing passes appeared sufficient for homogeneity. Viscosities and extrusion forces of CHM/lidocaine blends decrease with increasing amount of lidocaine. Needle jams do not increase. The pH and elasticity of the CHM/lidocaine blend are essentially equivalent to those of CHM alone. Epinephrine added to lidocaine did not alter the results enough to reach statistical significance. CONCLUSIONS Addition of lidocaine to original CHM can be safely added without harmful changes in physical properties of the original soft tissue filler. Further studies are required to explore whether the addition of lidocaine to CHM alters patient discomfort, durability, and efficacy.
Micrometer-Scale Magnetic-Resonance-Coupled Radio-Frequency Identification and Transceivers for Wireless Sensors in Cells (2017)

Forget inventory control in big-box stores---what if we had RFID chips to monitor $i\phantom{\rule{0}{0ex}}n\phantom{\rule{0}{0ex}}d\phantom{\rule{0}{0ex}}i\phantom{\rule{0}{0ex}}v\phantom{\rule{0}{0ex}}i\phantom{\rule{0}{0ex}}d\phantom{\rule{0}{0ex}}u\phantom{\rule{0}{0ex}}a\phantom{\rule{0}{0ex}}l$ $c\phantom{\rule{0}{0ex}}e\phantom{\rule{0}{0ex}}l\phantom{\rule{0}{0ex}}l\phantom{\rule{0}{0ex}}s$ in a living body? A team of researchers has started us on this road, by creating radio-frequency devices just 22 \textmu{}m across, which can be naturally taken up by live cells. Despite their size, these devices emit strong signals and can be sensed wirelessly by their corresponding transceivers. Their potential for continuous tracking of intracellular activities is quite significant for research and practice in biology and medicine.
<title>Advances in the development of the nested high-voltage generator</title> (1995)

The Nested High Voltage Generator (NHVG) is a high voltage accelerator/power supply topology which can potentially satisfy a variety of requirements for a compact, reliable inexpensive DC accelerator in the 0.25 10 MeV range. Applications for this technology include the generation of high voltage, high current pulsed electron beams for microwave generation (for example in the NLC or Next Linear Collider), medical product sterilization, polymer curing, waste water sterilization, waste water remediation, and medical waste sterilization. This technology has recently been demonstrated in an accelerator which has operated at 500 kV with an electron beam in a 36 inch long, 17 inch diameter device. In this paper, we briefly describe the technology, and the capabilities of our 500 kV machine. We also describe the capabilities of a machine of further reduced size.
Inactivation of the flax rust resistance gene M associated with loss of a repeated unit within the leucine-rich repeat coding region. (1997)

The M rust resistance gene from flax was cloned after two separate approaches, an analysis of spontaneous M mutants with an L6 gene-derived DNA probe and tagging with the maize transposon Activator, independently identified the same gene. The gene encodes a protein of the nucleotide binding site leucine-rich repeat class and is related (86% nucleotide identity) to the unlinked L6 rust resistance gene. In contrast to the L locus, which contains a single gene with multiple alleles, approximately 15 related genes occur at the complex M locus, with only one encoding the M resistance specificity. The M protein contains two direct repeats of 147 and 149 amino acids in the C-terminal part of the leucine-rich region. Three mutant alleles of M encoding a product containing a single repeat unit of 154 amino acids were isolated. The mutant DNA sequences probably occurred by unequal intragenic exchange in the coding region of the repeats. The recombinant alleles lost M resistance and gained no detectable new resistance specificity.
The Fate of Schwann Cell Basement Membranes in Permanently Transected Nerves (1990)

After peripheral nerve fiber degeneration, Schwann cell basement membranes (SCBM) persist, maintain the columnar orientation of multiplying Schwann cells, and provide pathways for regenerating axons to original target tissue. Despite the putative importance of these functions, there is little quantitative information on SCBM in chronic denervation. The number, integrity, shape, and size of SCBM were evaluated in transverse electron micrographs of peroneal nerves of groups of mice at various times after permanent sciatic nerve transection. With increasing time after transection, the SCBM fragment, the fragments become shorter, dispersed throughout the endoneurium and partially disappear. The discontinuity, dispersion, and partial disappearance of SCBM, which worsens with time after nerve transection, alters the scaffold by which neurites grow back to formerly innervated or appropriate target tissue. Without reaching appropriate target tissue, regenerating fibers may fail to develop or undergo retrograde atrophy and degeneration. The progressive changes of the SCBM may contribute to the demonstrated poor regeneration when nerve reconnection is delayed, or when proximal nerves are reconnected, so that much time may elapse before neurites grow back to distal nerve.
Single-cell Raman and fluorescence microscopy reveal the association of lipid bodies with phagosomes in leukocytes (2005)

Cellular imaging techniques based on vibrational spectroscopy have become powerful tools in cell biology because the molecular composition of subcellular compartments can be visualized without the need for labeling. Using high-resolution, nonresonant confocal Raman microscopy on individual cells, we demonstrate here that lipid bodies (LBs) rich in arachidonate as revealed by their Raman spectra associate with latex bead-containing phagosomes in neutrophilic granulocytes. This finding was corroborated in macrophages and in PLB-985 cells, which can be induced to differentiate into neutrophil-like cells, by selective staining of LBs and visualization by confocal fluorescence microscopy. We further show that the accumulation of LBs near phagosomes is mediated at least in part by the flavohemoprotein gp91phox (in which "phox" is phagocyte oxidase), because different LB distributions around phagocytosed latex beads were observed in WT and gp91phox-deficient PLB-985 cells. gp91phox, which accumulates in the phagosomal membrane, is the catalytic subunit of the leukocyte NADPH oxidase, a critical enzyme in the innate immune response. Finally, time-lapse fluorescence microscopy experiments on neutrophils revealed that the LB-phagosome association is transient, similar to the "kiss-and-run" behavior displayed by endosomes involved in phagosome maturation. Because arachidonic acid (AA) has been shown to be involved in NADPH oxidase activation and phagosome maturation in neutrophils and macrophages, respectively, the findings reported here suggest that LBs may provide a reservoir of AA for local activation of these essential leukocyte functions.
Prostate-specific membrane antigen is produced in tumor-associated neovasculature. (1999)

Prostate-specific membrane antigen (PSMA), a type II transmembrane protein, was originally thought to be strictly expressed in prostatic tissue, but recent studies have demonstrated PSMA protein expression in nonprostatic tumor neovasculature as well. Using immunohistochemistry, reverse transcription-PCR assays, and in situ hybridization, we have demonstrated PSMA mRNA transcripts and protein expression in the endothelium of tumor-associated neovasculature of multiple nonprostatic solid malignancies. In addition, we found no PSMA mRNA or protein expression in the vascular endothelial cells of corresponding benign tissue examples. Our findings expand the possible therapeutic role of PSMA and establish it as a unique biomarker specifically produced and expressed by tumor-associated neovasculature but not produced or expressed by normal vessels.
Numerical Modeling of Coanda Jet Controlled Nacelle Configurations (2004)

Modification of the aerodynamic characteristics of axisymmetric nacelles with the use of tangential Coanda jets is studied. It is demonstrated that Coanda jets in the leading edge (lip) region of the nacelle can increase the entrainment of air flowing into the nacelle. It is also shown that Coanda jets in the trailing edge region of the nacelle can laterally spread the jet-fan exhaust, and may lead to a reduction in the exhaust velocity downstream. The leading edge jet slot position was found to have a significant effect on the flow field. It is concluded that Coanda jets may be useful in altering and improving the performance of a nacelle that has been designed for cruise conditions.
Multiple elements in the 5' untranslated region down-regulate c-sis messenger RNA translation. (1995)

Expression of the platelet derived growth factor (PDGF) B-chain, the product of the c-sis proto-oncogene, is regulated both at the transcriptional and translational level. Previous studies have shown that the long 5' untranslated region (UTR) of the c-sis mRNA strongly inhibits synthesis of the PDGF-B chain. However, the assignments of down-regulatory regions within the 5' UTR were ambiguous. Expression of several site-directed point and deletion mutants of the 5' UTR of the c-sis mRNA in COS1 cells revealed that the UTR inhibited PDGF-B chain synthesis in a more complex manner than indicated by the previous studies. Abrogation of the three upstream short open reading frames by mutating each of the AUGs did not have any effect on the synthesis of the PDGF-B chain. Expression of deletion mutants revealed two partially overlapping regions, nucleotides 1-651 and 475-1022, each of which independently inhibited c-sis mRNA translation as effectively as the entire 5' UTR. Each of these regions contains a potentially strong stem-loop structure and a GC-rich element. These elements of the alternate down-regulatory regions could interact within the same region and/or with the elements of the other regulatory region to block c-sis mRNA translation. We show, in contrast to the previous reports, that the inhibition of c-sis mRNA translation cannot be attributed exclusively to any particular predicted secondary structure or a GC-rich element within the 5' UTR.(ABSTRACT TRUNCATED AT 250 WORDS)
Structure comparison of human glioma pathogenesis-related protein GliPR and the plant pathogenesis-related protein P14a indicates a functional link between the human immune system and a plant defense system (1998)

The human glioma pathogenesis-related protein (GliPR) is highly expressed in the brain tumor glioblastoma multiforme and exhibits 35% amino acid sequence identity with the tomato pathogenesis-related (PR) protein P14a, which has an important role for the plant defense system. A molecular model of GliPR was computed with the distance geometry program DIANA on the basis of a P14a-GliPR sequence alignment and a set of 1,200 experimental NMR conformational constraints collected with P14a. The GliPR structure is represented by a group of 20 conformers with small residual DIANA target function values, low AMBER-energies after restrained energy-minimization with the program OPAL, and an average rms deviation relative to the mean of 1.6 A for the backbone heavy atoms. Comparison of the GliPR model with the P14a structure lead to the identification of a common partially solvent-exposed spatial cluster of four amino acid residues, His-69, Glu-88, Glu-110, and His-127 in the GliPR numeration. This cluster is conserved in all known plant PR proteins of class 1, indicating a common putative active site for GliPR and PR-1 proteins and thus a functional link between the human immune system and a plant defense system.