gebhart/patrepeval huggingface dataset:
Aza-Crown Macrocycles (1993)

Preparation of Starting Materials. General Synthetic Methods for the Polyaza-Crown Macrocycles. Common Methods for the Formation of Polyaza Macrocyclic Rings. Monoaza-Crown Macrocycles. Diaza-Crown Macrocycles. Polyaza-Crown Macrocycles. Benzoaza-Crown Macrocycles. Aza-Crown Macrocycles Containing Other Heteroatoms in the Macroring. Aliphatic Peraza-Crown Macrocycles (Cyclams). Peraza-Cyclophanes. Aza- and Peraza-Crown Macrocycles as Part of Macromolecular Compounds. Some Practical Approaches to the Aza-Crown Macrocycles. Indexes.
Reported History of Childhood Abuse and Young Adults' Information-Processing Biases for Facial Displays of Emotion (2008)

The primary goal of this study was to examine the relations between young adults' reports of childhood abuse and their current attention and interpretation biases for facial displays of emotion. Consistent with prediction, individuals reporting a history of moderate to severe childhood abuse exhibited preferential attention to angry faces and increased sensitivity in the detection of angry expressions at lower levels of emotional intensity. Both the attention and interpretation biases were specific to angry rather than happy or sad faces. These results are consistent with the hypothesis that experiences of childhood abuse may contribute to the development of experience-specific information-processing biases.
Tomato Mutants Altered in Bacterial Disease Resistance Provide Evidence for a New Locus Controlling Pathogen Recognition (1994)

John M. Salmeron, Susan J. Barker, Francine M. Carland, Anand Y. Mehta, Brian J. Staskawicz, Tomato Mutants Altered in Bacterial Disease Resistance Provide Evidence for a New Locus Controlling Pathogen Recognition, The Plant Cell, Vol. 6, No. 4 (Apr., 1994), pp. 511-520
Expression of simian virus 40-rat preproinsulin recombinants in monkey kidney cells: use of preproinsulin RNA processing signals. (1981)

The complete rat preproinsulin gene I was cloned into a simian virus 30 (SV 40) vector. Most of the late region of the viral vector, including the SV40 intervening sequences (introns) and all of the major splice junctions, was deleted and replaced by the entire rat insulin gene. The recombinant molecules and a temperature-sensitive helper virus (tsA28) were inoculated into monkey kidney cultures. The formation of stable transcripts of the insulin insert was as efficient as the production of late SV40 mRNA. Analysis of these transcripts indicated that the rat preproinsulin gene nucleotide signals involved in RNA splicing and poly(A) addition were used. Examination of the 5' ends of the mRNAs showed several classes, one of which was the same size as the authentic rat insulinoma mRNA. This suggests that a portion of the transcripts may be initiated or processed faithfully, or both, at their 5' ends within rat insulin sequences. Significant quantities of a protein identified as rat proinsulin were synthesized. Detection of most of the proinsulin in the tissue culture medium suggests that this protein was secreted.
Interphase cytogenetics in paraffin embedded sections from human testicular germ cell tumor xenografts and in corresponding cultured cells. (1989)

A protocol was developed that allows determination of chromosome aberrations in interphase nuclei from paraffin embedded human tissues. As a model system tissue sections from xenografts derived from three testicular germ cell tumors (two teratocarcinoma and one embryonal carcinoma), as well as sections from normal intestine and testicular tissues, were hybridized with a biotin-labeled DNA probe specific for 1q12. For comparison, isolated nuclei in suspension and metaphase spreads from in vitro cell lines derived from the respective xenografts were assayed. Our results show that interphase tumor cells with aberrant numbers of chromosome 1 can be reliably detected both in vitro and in vivo. Subclones with two and three labeled chromosomes, respectively, could be defined and quantitatively evaluated. Present and future possibilities to pinpoint specific chromosome aberrations directly in cells present in body fluids or in tumor tissues are discussed.
Clustering and co-transcription of the Bacillus subtilis genes encoding the aminoacyl-tRNA synthetases specific for glutamate and for cysteine and the first enzyme for cysteine biosynthesis. (1994)

The Bacillus subtilis cysE and cysS genes encoding, respectively, the serine acetyltransferase and the cysteinyl-tRNA synthetase were found downstream from the gltX gene encoding the glutamyl-tRNA synthetase. This gene organization is also conserved in Bacillus stearothermophilus where the cysE and cysS genes show high amino acid identity with those of B. subtilis. In both organisms the coding sequences of cysE and cysS overlap, suggesting a translational coupling. B. subtilis cysE and cysS were expressed in Escherichia coli using the inducible trc promoter; they functionally complement mutants of E. coli affected in those genes. Overproduction of B. subtilis CysRS in E. coli has a toxic effect on cell growth. Disruption of gltX and cysS by Campbell-type insertion is lethal for the cell, indicating that these genes code for an essential and unique function in B. subtilis. S1 mapping analysis shows that the transcription of gltX is under the control of a sigma A promoter located 43 base pairs upstream of the initiation codon. A T-box sequence and a rho-independent terminator known to regulate expression of other aminoacyl-tRNA synthetase genes and of some amino acid biosynthetic operons in Bacillus sp., were found between gltX and cysE. No sigma A promoter was detected upstream of cysE, which is consistent with the lethality of a Campbell-type insertion using a plasmid that interrupts transcription coming from the gltX promoter, and suggests that gltX, cysE, and cysS constitute an operon. This is the first case where genes implicated in the biosynthesis of an amino acid and its cognate aminoacyl-tRNA synthetase are shown to be co-transcribed.
Biosensors--Sense and Sensitivity (2000)

Biosensors are a cunning combination of biological molecules and microelectronics that can be used to measure blood glucose levels, pollutants in the environment or food-borne pathogens in the food supply. In a comprehensive TechView, Anthony Turner takes us on a tour of historical developments and the latest innovations in biosensor research.
THE IN VIVO ANTITUMORAL EFFECTS OF LIPOPOLYSACCHARIDE AGAINST GLIOBLASTOMA MULTIFORME ARE MEDIATED IN PART BY TOLL-LIKE RECEPTOR 4 (2007)

LPS-induced antitumoral effects on glioblastoma multiforme are mediated, in part, by the Tlr-4 receptor. Further understanding of this process may lead to novel treatment strategies for this uniformly fatal disease.
Antibodies to synthetic peptides as probes of acetylcholine receptor structure (1984)

Peptides containing the C-terminus of the alpha-chain of the nicotinic acetylcholine receptor (nAChR), as deduced from cDNA data, were synthesised and shown to bind to antibodies to denatured nAChR. Conversely, peptide-specific antibodies bound both to native and to denatured nAChR. Binding was exclusively to the alpha-chain. Trypsinization experiments and the use of the unique C-terminal hexapeptide of the alpha-chain demonstrated that the proposed C-terminus does exist on the mature alpha-chain, and that post-translational cleavage can be discounted as an explanation of the discrepancy of the molecular masses of the alpha-chain deduced from SDS gel electrophoresis (40 kDa) and from the DNA sequencing (50 kDa). Cleavage of the alpha-chain in the membrane occurs at two closely linked sites, resulting in the formation of a large fragment (approximately 35 kDa) and the remainder of the chain (approximately 9-10 kDa). No signs of experimental myasthenia gravis were observed in rabbits immunised with C-terminal peptide coupled to carrier protein.
The Clinical Time-Course of Experimental Autoimmune Uveoretinitis Using Topical Endoscopic Fundal Imaging with Histologic and Cellular Infiltrate Correlation (2008)

In EAU, there is a strong correlation between histologic severity and the number of infiltrating leukocytes into the retina. TEFI enhances the monitoring of clinical disease in a rapid and noninvasive fashion. Full assessment of preclinical immunotherapeutic efficacy requires the use of all three parameters: TEFI, histologic assessment, and flow cytometric analysis of retinal infiltrate.
Purification and characterization of a periplasmic oligopeptide binding protein from Escherichia coli. (1985)

We have purified and characterized an oligopeptide binding protein released from the periplasm of Escherichia coli W by mild osmotic shock. The purified protein was greater than 97% homogeneous as determined by either sodium dodecyl sulfate-polyacrylamide gel electrophoresis (Mr = 60,000) or isoelectric focusing (pI = 5.95). The binding protein has a Stokes radius of 30 A and a sedimentation coefficient (s(0)20,w) of 4.6 S. Based on these hydrodynamic studies, the native protein has a molecular weight of 56,000. The tripeptide, Ala-Phe-[3H]Gly, which is transported via the shock-sensitive sensitive oligopeptide permease, binds to the purified protein in dilute solution with a Kd of 0.1 microM and a stoichiometry of approximately 1 to 1. Results from this study support the hypothesis that this periplasmic oligopeptide binding protein functions in the initial recognition of peptide substrates for the oligopeptide permease system.
Knowledge representation, connectionism and conceptual retrieval (1988)

Knowledge Representation (KR) systems provide support for Artificial Intelligence systems that reason about relationships between objects in their domains of expertise. Because of their support for inference, KR systems appear to have potential to enrich the kind of retrievals that IR systems might make. Ironically, however, the most useful KR systems are limited to reasoning based on a rigid notion of validity, and thus are awkward to use when relevant but inexact retrievals are desired. We have been exploring the potential of a “connectionist” model—the Boltzmann Machine—to overcome this limitation. We report on a number of experiments in which we use a connectionist simulator to support similarity-based reasoning in a frame representation. We draw some tentative, mixed conclusions on the potential for a union of KR, IR, and connectionism.
Amniotic membrane transplantation for ocular surface reconstruction (1999)

AMT was effective to promote corneal healing in patients with persistent epithelial defect, and appeared to be helpful after surgery to release corneo-conjunctival adhesion. Most cases required further surgery for visual and ocular surface rehabilitation. Amniotic membrane used as a patch was not effective to prevent tectonic corneal graft in cases with severe stromal thinning and impending or recent perforation.
BRAF mutations in papillary thyroid carcinoma. (2006)

Papillary thyroid carcinoma (PTC) is the most frequent malignant neoplasm of the thyroid originating from the thyroid follicular cell (TFC). Although the formation of PTC is believed to result from rearrangements of RET or TRK oncogenes or MET point mutations, these structural aberrations or point mutations do not correlate with the clinicopathological features of PTC and do not seem to be a useful prognostic marker of the disease. Therefore, further experiments should be carried out in order to find new practical clinical markers. Recently, oncogene BRAF has become a subject of great interest. The mutation of BRAF gene is characteristic for PTC and poorly differentiated and/or undifferentiated cancers derived from PTC. The occurrence of BRAF mutation has often been observed in various human tumours. The presence of mutation was confirmed in melanoma, colon cancer, gliomas and lung cancer. In the majority of cases, there is only one type of point mutation - V600E. The RAS/RAF/MEK/MAPK kinase pathway mediates the cellular response to mitogenic signals. BRAF gene mutation results in increased kinase activity, leading to excessive activation of the above mitogenic pathway and to uncontrolled proliferation of cancer cells. Some correlation was noticed between BRAF gene mutation and the clinical stage of the neoplastic disease in question. Preliminary investigations indicate that the presence of BRAF mutation might be a valuable diagnostic and prognostic marker of the disease. Further investigations could also bring further improvements into the therapeutic management of thyroid cancer. There are reports emphasizing the possibility of using the inhibitors of BRAF proteins in the treatment of PTC. Certainly, in order to confirm the diagnostic usefulness of this marker, further studies should be carried out.
Novel approaches to treat oxidative stress and cardiovascular diseases. (2007)

Reduction-oxidation (redox) reactions that generate reactive oxygen species (ROS) such as hydrogen peroxide and superoxide have been identified as important chemical processes that regulate signal transduction. The findings of increased ROS in association with endothelial dysfunction has given rise to the "antioxidant hypothesis": since ROS are increased in hypertension, atherosclerosis and vascular injury, then inhibiting oxidative stress with antioxidants should decrease cardiovascular events. Preliminary efforts with antioxidant vitamins like beta-carotene, vitamin C and vitamin E have shown no clinical benefits. Here we discuss a specific "redox signaling hypothesis." We propose that physiologic stimuli such as steady laminar flow regulate the redox state of cells and tissues thereby modulating signaling molecules that are redox sensitive. Here we show that steady laminar flow inhibits tumor necrosis factor (TNF) signaling and inflammation in endothelial cells. We have identified a specific redox molecule-thioredoxin interacting protein (TXNIP)-as a key redox regulator of inflammation in blood vessels. We suggest that modifying the redox state of the vasculature is an attractive therapeutic approach if we target specific redox dependent pathways such as TXNIP.
Multiple Alignment of DNA Sequences with MAFFT (2009)

Multiple alignment of DNA sequences is an important step in various molecular biological analyses. As a large amount of sequence data is becoming available through genome and other large-scale sequencing projects, scalability, as well as accuracy, is currently required for a multiple sequence alignment (MSA) program. In this chapter, we outline the algorithms of an MSA program MAFFT and provide practical advice, focusing on several typical situations a biologist sometimes faces. For genome alignment, which is beyond the scope of MAFFT, we introduce two tools: TBA and MAUVE.
Protein C-mannosylation: facts and questions. (2000)

Among the posttranslational modifications of proteins, glycosylation is probably the most abundant one. Two main types of protein glycosylation have been known for several years, namely N-glycosylation and O-glycosylation. Their biochemical properties, structure and biosynthesis, have been described extensively. Their biological functions are also known for a number of proteins, although in many cases the function remains speculative despite continuous efforts. A few years ago, a new type of protein glycosylation was found, which is different from the above-mentioned ones. It was called C-glycosylation, since the sugar is linked to the protein through a carbon-carbon bond. This article reviews the biochemistry of C-glycosylation, the biosynthetic pathway and structural requirements. Possible biological functions of this modification are also discussed.
NH2-terminal modification of the phosphatase 2A catalytic subunit allows functional expression in mammalian cells. (1992)

Functional expression of recombinant wild-type phosphatase 2A catalytic subunit has been unsuccessful in the past. A nine-amino-acid peptide sequence (YP-YDVPDYA) derived from the influenza hemagglutinin protein was used to modify the NH2 and/or COOH terminus of the phosphatase 2A catalytic subunit. Addition of the nine-amino-acid sequence at the NH2 terminus allowed recombinant phosphatase 2A expression as a predominantly cytosolic phosphatase 2A enzyme. The 12CA5 monoclonal antibody that recognizes the nine-amino-acid hemagglutinin peptide sequence was used to immunoprecipitate the epitope-tagged phosphatase 2A catalytic subunit. Assay of the immunoprecipitated epitope-tagged phosphatase 2A demonstrated an okadaic acid-sensitive dephosphorylation of [32P] histone H1 and [32P]myelin basic protein similar to that measured with the wild-type enzyme. Functional phosphatase activity could be demonstrated for the NH2-terminal modified phosphatase 2A catalytic subunit following transient expression in COS cells or stable expression in Rat1a cells. In contrast, the COOH-terminal-modified phosphatase 2A catalytic subunit was very poorly expressed. The NH2-, COOH-modified subunit, having the nine-amino-acid hemagglutinin peptide sequence encoded at both termini of the polypeptide, was also expressed as a functional phosphatase 2A enzyme. Thus, NH2-terminal modification of the phosphatase 2A catalytic subunit results in a functional plasmid-expressed enzyme. The unique nine-amino-acid epitope-tag sequence also provides a method to easily resolve the recombinant phosphatase 2A from the endogenous wild-type gene product and related phosphatases expressed in cells.
Biofuels in the environment : a review of behaviours, fates, effects and possible remediation techniques (2009)

The use of biofuels is being promoted as an alternative to conventional petroleum fuels. It is likely that increased use of biofuels will result in an increase in spills to the aquatic and terrestrial environment. Although many claims are made that biofuels are environmentally friendly and non toxic, the introduction of biofuel blends into fuels changes their physical properties and chemical makeup, thereby changing the effectiveness of current spill mitigation and clean-up procedures. As such, well-developed spill response and remediation technologies specific to biofuels and biofuel blends will be needed to support the development of the biofuel industry. This study focused on the interactions of biological and petroleum fuels in the environment, with particular reference to the behaviour of large spills in the environment, their persistence and the risk they pose to ecosystems. The paper highlighted existing knowledge gaps in biofuel chemical composition, fate, behaviour and toxicity in the environment and in spill response and remediation technologies. It considered biodiesels, vegetable oils, ethanol and ethanol-gasoline blends. Preliminary studies have demonstrated that dispersion exposure routes can lead to acute toxicities in some species. Vegetable oil spills have had significant impacts on wildlife because they are not soluble in water, do not evaporate, do not form water-in-oil emulsions and do not disperse in water. Mechanical recovery and sorbent use were the 2 spill response operations considered in this paper, while site cleanup and remediations options included land-farming, multi-phase extraction and in-situ chemical oxidation. 31 refs.
A hydrogel-based microfluidic device for the studies of directed cell migration (2007)

We have developed a hydrogel-based microfluidic device that is capable of generating a steady and long term linear chemical concentration gradient with no through flow in a microfluidic channel. Using this device, we successfully monitored the chemotactic responses of wildtype Escherichia coli (suspension cells) to α-methyl-DL-aspartate (attractant) and differentiated HL-60 cells (a human neutrophil-like cell line that is adherent) to formyl-Met-Leu-Phe (f-MLP, attractant). This device advances the current state of the art in microchemotaxis devices in that (1) it demonstrates the validity of using hydrogels as the building material for a microchemotaxis device; (2) it demonstrates the potential of the hydrogel based microfluidic device in biological experiments since most of the proteins and nutrients essential for cell survival are readily diffusible in hydrogel; (3) it is capable of applying chemical stimuli independently of mechanical stimuli; (4) it is straightforward to make, and requires very basic tools that are commonly available in biological labs. This device will also be useful in controlling the chemical and mechanical environment during the formation of tissue engineered constructs.
Nature of Alumina in Phosphate Glass: I, Properties of Sodium Aluminophosphate Glass (1993)

Glasses along four compositional tie lines, I: xAl(PO 3 ) 3 ’(1 – x)NaPO 3 , II: xAlPO 4 ′(1 – x)NaPO 3 , III: xAl 2 O 3 ′(1 – x)NaPO 3 , and IV: xNaAlO 2 ,(1 – x)NaPO 3 , have been prepared and a number of their properties evaluated. In general, Al 2 O 3 additions increase the glass transition temperature, decrease thermal expansion, and improve aqueous durability. However, the composition/property relationships are strongly influenced by relative cation ratios and thus the overall O/P ratio. The nature of these glasses undergoes significant transformations at both the pyrophosphate (O/P = 3.5) and the orthophosphate (O/P = 4.0) compositions, producing significant changes in the property behavior. Spectroscopic analyses of glass structure, described in part II of this report, reveal that changes in Al coordination coincide with the breaks in the property behavior.
Autocatalytic activity of the tobacco etch virus NIa proteinase in viral and foreign protein sequences (1992)

The small nuclear inclusion (NIa) protein of the tobacco etch virus (TEV) is synthesized initially as part of a genome-derived high M(r) precursor. The NIa protein releases itself from this genome-derived precursor by self-cleavage, or an autocatalytic processing event. Cleavage between specific glutamine-glycine dipeptides at the N and C termini generates the 430 amino acid or 49,000 M(r) (49K) NIa protein. The requirements of this autocatalytic release, or cis cleavage, were examined by constructing gene cassettes encoding the TEV NIa protein which could be ligated into particular locations in cDNA of the TEV genome and also into foreign gene DNA sequences. Using cell-free transcription and translation systems, polyproteins containing TEV NIa sequences were synthesized and assayed for (i) autocatalysis and (ii) the ability of a functional NIa proteinase, purified from plant tissue, to cleave in bimolecular or trans reactions various artificial polyproteins which contained an inactive form of the NIa proteinase. The NIa self-cleavage events required an active proteinase sequence and a consensus TEV cleavage site sequence at the N and C termini. These results were consistent for NIa protein sequences placed at a foreign TEV cleavage site or in unrelated proteins. Differences were noted in the trans cleavage of these sites.