gebhart/patrepeval huggingface dataset:
Human 18 S ribosomal RNA sequence inferred from DNA sequence. Variations in 18 S sequences and secondary modification patterns between vertebrates (1985)

We have determined the DNA sequences encoding 18 S ribosomal RNA in man and in the frog, Xenopus borealis. We have also corrected the Xenopus laevis 18 S sequence: an A residue follows G-684 in the sequence. These and other available data provide a number of representative examples of variation in primary structure and secondary modification of 18 S ribosomal RNA between different groups of vertebrates. First, Xenopus laevis and Xenopus borealis 18 S ribosomal genes differ from each other by only two base substitutions, and we have found no evidence of intraspecies heterogeneity within the 18 S ribosomal DNA of Xenopus (in contrast to the Xenopus transcribed spacers). Second, the human 18 S sequence differs from that of Xenopus by approx. 6.5%. About 4% of the differences are single base changes; the remainder comprise insertions in the human sequence and other changes affecting several nucleotides. Most of these more extensive changes are clustered in a relatively short region between nucleotides 190 and 280 in the human sequence. Third, the human 18 S sequence differs from non-primate mammalian sequences by only about 1%. Fourth, nearly all of the 47 methyl groups in mammalian 18 S ribosomal RNA can be located in the sequence. The methyl group distribution corresponds closely to that in Xenopus, but there are several extra methyl groups in mammalian 18 S ribosomal RNA. Finally, minor revisions are made to the estimated numbers of pseudouridines in human and Xenopus 18 S ribosomal RNA.
A family of luminescent coordination compounds: iridium(iii) polyimine complexes (2000)

30 years of IrIII coordination chemistry with polyimine-type ligands are summarized. Over the years, milder reaction conditions have been used for their synthesis, allowing the incorporation of various functional substituents. Complexes are described with bidentate and terdentate ligands, with both N- and C-donor sites. All complexes are luminescent, with predominantly charge-transfer or ligand-centred emissive states depending on the charge density donated from the ligands to the metal. IrIII excited state lifetimes range from nanoseconds to microseconds. A wide range of properties are obtained: [IrN6]3+ complexes are strong photooxidants while tris-cyclometallated [IrN3C3] complexes are strong photoreductants.
Comparison of phytase from genetically engineered Aspergillus and canola in weanling pig diets. (2000)

Ninety-six crossbred pigs with an average weight of 9.0 kg were used in a 5-wk trial to compare the efficacy of genetically engineered Aspergillus ficuum phytase, expressed in Aspergillus niger (Natuphos) or in canola seed (Phytaseed), for enhancing the utilization of phytate P in corn-soybean meal-based diets fed to young pigs and to evaluate the safety of Phytaseed phytase. Three levels of the two sources of phytase (250, 500, or 2,500 U/kg of diet) were added to a corn-soybean meal basal diet containing .35% total P, .09% available P, and .50% Ca. There were six pens per treatment (one barrow and one gilt/pen), except that the diet without added phytase was fed to 12 pens of pigs. Pen feed consumption and BW were recorded weekly. During wk 5, pen fecal samples were collected for determination of apparent digestibilities of DM, Ca, and P. At the end of wk 5, all barrows were killed, and the 10th rib on both sides was removed for determination of shear force and energy. Thirty pigs (six from the diet without added phytase and the diets with 500 and 2,500 U/kg phytase from both sources) were randomly selected for gross necropsy and histologic evaluation of liver, kidney, and bone tissues. Both sources of phytase were equally effective in increasing (P < .05) daily gain, gain:feed, apparent digestibilities of DM, P, and Ca, and 10th rib measurements. Fecal P excretion was reduced with phytase addition. Feed intake was increased by phytase levels during wk 4 to 5. No significant abnormalities were seen in any of the 30 pigs necropsied. The fit of a nonlinear function revealed that most measurements were reaching a plateau at 2,500 U/kg phytase. In summary, based on performance, bone measurements, and digestibilities of P, Ca, and DM of young pigs, the efficiency of Phytaseed was similar to that of Natuphos for enhancing the utilization of phytate P in corn-soybean meal-based diets. General necropsy and histologic examination of tissues indicated no toxic effect of phytase.
Ca and O ion implantation doping of GaN (1996)

p- and n-type doping of GaN have been realized by ion implantation of Ca and O, respectively. Rapid thermal annealing at 1100 °C or higher is required to achieve p-type conduction in Ca or Ca+P implanted samples with an estimated ionization level of 169 meV and a corresponding activation efficiency of ∼100%. This is the first experimental report of an acceptor species in GaN, other than Mg, with an ionization energy level less than 180 meV. O-implanted GaN displays an ionization level of ∼29 meV but with an activation efficiency of only 3.6% after a 1050 °C anneal that may result from insufficient vacancy generation for the lighter O ion or from the existence of a second, deeper O energy level. Neither Ca or O displayed measurable redistribution, based on secondary ion mass spectrometry measurements, even after a 1125 °C anneal.
Relationships between the fan Allele and Agronomic Traits in Soybean (1993)

Normal levels of linolenic acid (70‐80 g kg ‐1 ) in soybean [ Glycine max (L.) Merr.] oil adversely affect oil flavor and stability. The mutation‐induced line C1640 has half the normal level of linolenic acid (37 g kg ‐1 ), but is 24% lower yielding than ‘Century’, from which it was selected. This study was conducted to determine if there are genetic relationships betweena gronomictr aits and the fan allele for low linolenic acid identified in C1640. Century and ‘Harper’, both with the FanFan alleles for normal 18:3, were crossed with C1640 containing the fanfan alleles for low 18:3. Both FanFan and fanfan segregates from the two crosses were evaluated for agronomic traits and linolenic acid in replicated tests over a 2‐yr period on a Chalmers soil (fine‐silty, mixed, mesic Typic Haplaquoll) at the Purdue University Agronomy Research Center near West Lafayette, IN. The fanfan segregates in the Century × C1640 cross averaged slightly higher in seed yield and taller in plant height than the FanFans egregates. In the Harper × C1640 cross, fanfan segregates averaged 1 d later in maturity than FanFan segregates. Mean values for FanFan and fanfan segregates for other traits in both crosses were essentially the same. These data indicate that there are no associations between the fanfan alleles and those agronomic traits needed in commercial soybean cultivars with low levels of linolenic acid. Apparently the low yield of C1640 is controlled by genetic changes independent of the mutation for low 18:3. Regression of linolenic acid level on maturity dates for both FanFan and fanfan segregates in the Harper × C1640 cross show that segregates of both genotypes tended to have increased linolenic acid at later maturity dates. This could be attributed to the cooler temperatures during seed maturation to which the later maturing segregates were exposed.
Carp Muscle Calcium-binding Protein (1973)

The structure of crystalline carp muscle calcium-binding protein (parvalbumin) has been determined by x-ray diffraction techniques to nominal 1.85-A resolution. Isomorphous and anomalous scattering data were measured for three heavy atom derivatives, 3-chloromercuri-2-methoxypropyl urea, mercury bromide, and ethyl mercury chloride, to 2.0-A resolution using precession photography. As described in Paper III in this series the 2.0-A phases were refined and the 2.0- to 1.85-A phases were determined by use of the tangent formula. The electron density map is interpreted in terms of the 108 amino acid sequence described in Paper I in this series. A calcium ion is bound in the loop between helix C and helix D and a second calcium is bound in the EF loop. The entire CD region is related to helix E, the EF loop, and the terminal helix F by an approximate intramolecular 2-fold axis. Although it does not bind calcium the AB region has a structure similar to the CD and EF regions and appears to have resulted from a gene triplication. The molecule is generally spherical with a well defined hydrophobic core, one-seventh of its total volume, composed of side chains of phenylalanine, isoleucine, leucine, and valine. All of the polar side chains are at the surface except those associated with calcium binding and with an invariant internal salt bridge between arginine-75 and glutamic acid-81.
Refined structure of dimeric diphtheria toxin at 2.0 Å resolution (1994)

The refined structure of dimeric diphtheria toxin (DT) at 2.0 A resolution, based on 37,727 unique reflections (F > 1 sigma (F)), yields a final R factor of 19.5% with a model obeying standard geometry. The refined model consists of 523 amino acid residues, 1 molecule of the bound dinucleotide inhibitor adenylyl 3'-5' uridine 3' monophosphate (ApUp), and 405 well-ordered water molecules. The 2.0-A refined model reveals that the binding motif for ApUp includes residues in the catalytic and receptor-binding domains and is different from the Rossmann dinucleotide-binding fold. ApUp is bound in part by a long loop (residues 34-52) that crosses the active site. Several residues in the active site were previously identified as NAD-binding residues. Glu 148, previously identified as playing a catalytic role in ADP-ribosylation of elongation factor 2 by DT, is about 5 A from uracil in ApUp. The trigger for insertion of the transmembrane domain of DT into the endosomal membrane at low pH may involve 3 intradomain and 4 interdomain salt bridges that will be weakened at low pH by protonation of their acidic residues. The refined model also reveals that each molecule in dimeric DT has an "open" structure unlike most globular proteins, which we call an open monomer. Two open monomers interact by "domain swapping" to form a compact, globular dimeric DT structure. The possibility that the open monomer resembles a membrane insertion intermediate is discussed.
Microstructure of vapor-deposited optical coatings (1984)

The microstructure of thin films applied by conventional physical vapor deposition for use as optical coatings is columnar for most of the materials commonly used. This has been established for about a decade through numerous experimental observations employing microfractographical replication for use with high resolution transmission electron microscopes. Scanning electron microscopes are more useful investigating coating defects, the most remarkable of these defects being known as nodules. From fundamental considerations of nucleation and growth of thin films, the origin of both columns and nodules and the dependence of their appearance on the deposition conditions are discussed in some detail. A simple 2-D simulation model assuming limited surface mobility of adatoms or admolecules shows striking similarities to peculiar properties of both columnar and nodular growth seen in actual investigations. Conclusions are drawn as to how the two types of microstructure influence general film properties and, in particular, how they influence possible laser damage mechanisms.
An overview of methods and tools for ontology learning from texts (2004)

Ontology learning aims at reducing the time and efforts in the ontology development process. In recent years, several methods and tools have been proposed to speed up this process using different sources of information and different techniques. In this paper, we have reviewed 13 methods and 14 tools for semi-automatically building ontologies from texts and their relationships with the techniques each method follows. The methods have been grouped according to the main techniques followed and three groups have been identified: one based on linguistics, one on statistics, and one on machine learning. Regarding the tools, the criterion for grouping them, which has been the main aim of the tool, is to distinguish what elements of the ontology can be learned with each tool. According to this, we have identified three kinds of tools: tools for learning relations, tools for learning new concepts, and assisting tools for building up taxonomies.
The Session Initiation Protocol: Internet-centric signaling (2000)

The Session Initiation Protocol (SIP) provides advanced signaling and control functionality for a wide variety of multimedia services. SIP can efficiently and scalably locate resources based on a location-independent name and then negotiate session characteristics. It can find use in applications ranging from Internet telephony and conferencing to instant messaging, event notification, and the control of networked devices. We summarize the main protocol features and describe a range of extensions currently being discussed within the Internet Engineering Task Force.
Interaction of influenza virus hemagglutinin with a lipid monolayer. A comparison of the surface activities of intact virions, isolated hemagglutinins, and a synthetic fusion peptide (1991)

In the infectious entry pathway of influenza virus, the low pH of the endosomal compartment induces an irreversible conformational change in influenza virus hemagglutinin, leading to fusion of viral and endosomal membranes. In the current report, we characterized the low-pH-induced activation of hemagglutinin of influenza strain X31 by studying its interaction with a lipid monolayer. The surface activities of virions, of isolated hemagglutinins and its proteolytic fragments, and of a synthetic peptide mimicking the amino terminus of subunit 2 of hemagglutinin are compared. The data indicate that the surface activity of both virions and isolated hemagglutinin develop as a result of the low-pH-induced conformational change in hemagglutinin. The surface activity of isolated hemagglutinin is mainly caused by penetration into the lipid monolayer of protein domains other than the amino terminus of subunit 2 of hemagglutinin; domains in subunit 1 may be involved. The surface activity of virions appears to be a secondary effect of the conformational change and is explained by assuming a net transfer of viral lipids to the lipid monolayer.
Human monocyte adherence: a primary effect of chemotactic factors on the monocyte to stimulate adherence to human endothelium. (1987)

Monocyte emigration into areas of inflammation is initiated by monocyte adherence to the microvascular endothelium which may be induced by the local production of chemotactic factors at the inflammatory site. However, it is not clear whether such stimuli act on the monocyte and/or the endothelial cell to promote this effect. Accordingly, the effect of the chemotactic peptides C5a des arg and formyl-methionyl-leucyl-phenylalanine (FMLP) on human monocyte adherence to human microvascular endothelial cell monolayers was investigated in vitro. Monocytes (92 to 98% pure) were isolated by discontinuous plasma-Percoll density gradients and cell elutriation, methods designed to minimize monocyte exposure to endotoxin. Mean spontaneous (unstimulated) adherence of 111Indium-tropolonate-radiolabeled monocytes to microvascular endothelial cell monolayers was 19.7% +/- 1.3. Monocyte adherence to microvascular endothelial cell monolayers was stimulated in a dose-response fashion in the presence of C5a des arg or FMLP to a maximum mean adherence of 47.2% +/- 2.9 or 43.8% +/- 2.2, respectively. C5a des arg or FMLP stimulated monocytes to adhere to monolayers of human vascular smooth muscle cells, human dermal fibroblasts, or serum-coated plastic wells in a comparable fashion as to endothelial cells. The simultaneous presence of both chemotactic peptides C5a des arg and FMLP in the assay system stimulated monocyte adherence to the same degree as either stimulus alone. This finding suggested that those monocytes stimulated to adhere by C5a des arg were the same subpopulation responding to FMLP. Spontaneous monocyte adherence (in the absence of chemotactic peptides) to both endothelial cell monolayers and serum-coated plastic wells was reduced in the presence of plasma, but chemotactic peptides induced a significant, albeit reduced, adhesion of monocytes in this circumstance. The pretreatment of monocytes with either C5a des arg or FMLP prior to the adherence assay induced stimulus-specific desensitization of monocyte adherence. Neither a desensitization nor stimulated monocyte adherence occurred when endothelial cell monolayers or serum-coated plastic wells were pretreated with either of the chemotactic peptides. The fixation of endothelial cell monolayers prior to the adherence assay did not alter the degree of spontaneous, C5a des arg-stimulated, or FMLP-stimulated monocyte adherence. These data suggest that the stimulated adhesion of monocytes to endothelial cells by C5a des arg or FMLP represents primarily an effect of these chemotactic peptides on the monocyte.
A Comprehensive Strategy to Combat Colon Cancer Targeting the Adenomatous Polyposis Coli Tumor Suppressor Gene (2005)

Somatic cells in the majority of colorectal polyps and cancers contain mutations/deletions in the adenomatous polyposis coli (APC) tumor suppressor gene. APC is involved in normal intestinal development and acts to influence a variety of cellular processes. Loss of APC function leads to intestinal neoplasia in both mice and humans. APC influences expression of specific genes, including the c-Myc oncogene, which functions as a transcriptional activator. Loss of APC function leads to alterations in c-Myc-regulated genes including ornithine decarboxylase (ODC), the first enzyme in polyamine synthesis. A single nucleotide polymorphism (SNP) in the ODC promoter affecting c-Myc-dependent expression has been associated with risk of colorectal and other cancers. Pharmaceuticals that target structural features of the c-Myc promoter, and suppress expression of c-Myc and other genes regulated by similar promoter elements, are being developed as potential colorectal cancer chemotherapies. Difluoromethylornithine (DFMO), a selective inhibitor of ODC, is under clinical evaluation as a colorectal cancer chemopreventive agent. APC and APC-dependent genes, such as c-Myc and ODC, may be useful as genetic markers of risk and as targets for chemoprevention and therapy for colorectal cancer.
Curcumin: Getting Back to the Roots (2005)

The use of turmeric, derived from the root of the plant Curcuma longa, for treatment of different inflammatory diseases has been described in Ayurveda and in traditional Chinese medicine for thousands of years. The active component of turmeric responsible for this activity, curcumin, was identified almost two centuries ago. Modern science has revealed that curcumin mediates its effects by modulation of several important molecular targets, including transcription factors (e.g., NF-kappaB, AP-1, Egr-1, beta-catenin, and PPAR-gamma), enzymes (e.g., COX2, 5-LOX, iNOS, and hemeoxygenase-1), cell cycle proteins (e.g., cyclin D1 and p21), cytokines (e.g., TNF, IL-1, IL-6, and chemokines), receptors (e.g., EGFR and HER2), and cell surface adhesion molecules. Because it can modulate the expression of these targets, curcumin is now being used to treat cancer, arthritis, diabetes, Crohn's disease, cardiovascular diseases, osteoporosis, Alzheimer's disease, psoriasis, and other pathologies. Interestingly, 6-gingerol, a natural analog of curcumin derived from the root of ginger (Zingiber officinalis), exhibits a biologic activity profile similar to that of curcumin. The efficacy, pharmacologic safety, and cost effectiveness of curcuminoids prompt us to "get back to our roots."
Mosaicism of activatingFGFR3 mutations in human skin causes epidermal nevi (2006)

Epidermal nevi are common congenital skin lesions with an incidence of 1 in 1,000 people; however, their genetic basis remains elusive. Germline mutations of the FGF receptor 3 (FGFR3) cause autosomal dominant skeletal disorders such as achondroplasia and thanatophoric dysplasia, which can be associated with acanthosis nigricans of the skin. Acanthosis nigricans and common epidermal nevi of the nonorganoid, nonepidermolytic type share some clinical and histological features. We used a SNaPshot multiplex assay to screen 39 epidermal nevi of this type of 33 patients for 11 activating FGFR3 point mutations. In addition, exon 19 of FGFR3 was directly sequenced. We identified activating FGFR3 mutations, almost exclusively at codon 248 (R248C), in 11 of 33 (33%) patients with nonorganoid, nonepidermolytic epidermal nevi. In 4 of these cases, samples from adjacent histologically normal skin could be analyzed, and FGFR3 mutations were found to be absent. Our results suggest that a large proportion of epidermal nevi are caused by a mosaicism of activating FGFR3 mutations in the human epidermis, secondary to a postzygotic mutation in early embryonic development. The R248C mutation appears to be a hot spot for FGFR3 mutations in epidermal nevi.
Localization and cellular sources of activins in normal and fibrotic rat liver (1997)

1) while activin A was constitutively expressed in PC of normal liver, its expression was lost in PC of fibrotic liver; 2) expression of activins was induced in activated SC; and 3) apoptotic cells were found predominantly near the septa, in support of the hypothesis that activin A, derived from activated SC in the septa, contributes to the induction of cell death in neighboring PC.
Academy calls on federal government to clarify Medicaid benefits (2006)

The Academy has been urging the federal government to clarify the Medicaid benefits children can receive since the Deficit Reduction Act (DRA) passed Feb. 8. In the meantime, implementation is under way in several states.

The DRA gives states the option to change their Medicaid program by allowing
Preparation of Poly(A)+RNA (1993)

Most messenger RNAs contain a poly(A) tail, while structural RNAs do not. Poly(A) selection therefore enriches for messenger RNA. The technique has proved essential for construction of cDNA libraries. It is also useful when analyzing the structure of low-abundance mRNAs. Removing the ribosomal and tRNAs from a preparation increases the amount of RNA that can be clearly analyzed by S1 analysis, for example, thus allowing detection of a low level message. This protocol separates poly(A)+ RNA from the remainder of total RNA, which is largely rRNA and tRNA. Total RNA is denatured to expose the poly(A) (polyadenylated) tails. Poly(A)-containing RNA is then bound to oligo(dT) cellulose, with the remainder of the RNA washing through. The poly(A)+ RNA is eluted by removing salt from the solution, thus destabilizing the dT:rA hybrid. The column can then be repeated to remove contaminating poly(A)- RNA.