gebhart/patrepeval huggingface dataset:
Nonsense and missense mutations in hemophilia A: estimate of the relative mutation rate at CG dinucleotides. (1988)

Hemophilia A is an X-linked disease of coagulation caused by deficiency of factor VIII. Using cloned cDNA and synthetic oligonucleotide probes, we have now screened 240 patients and found CG-to-TG transitions in an exon in nine. We have previously reported four of these patients; and here we report the remaining five, all of whom were severely affected. In one patient a TaqI site was lost in exon 23, and in the other four it was lost in exon 24. The novel exon 23 mutation is a CG-to-TG substitution at the codon for amino acid residue 2166, producing a nonsense codon in place of the normal codon for arginine. Similarly, the exon 24 mutations are also generated by CG-to-TG transitions, either on the sense strand producing nonsense mutations or on the antisense strand producing missense mutations (Arg to Gln) at position 2228. The novel missense mutations are the first such mutations observed in association with severe hemophilia A. These results provide further evidence that recurrent mutations are not uncommon in hemophilia A, and they also allow us to estimate that the extent of hypermutability of CG dinucleotides is 10-20 times greater than the average mutation rate for hemophilia A.
The negative regulator of Î²-lactamase induction AmpD is a N-acetyl-anhydromuramyl-L-alanine amidase (1994)

Construction of a malE-ampD gene fusion allowed purification of biologically active fusion protein by affinity chromatography. The cloned malE-ampD gene fusion complemented a chromosomal ampD mutation. Purified MalE-AmpD fusion protein was found to have murein amidase activity with a pronounced specificity for 1,6-anhydromuropeptides, the characteristic murein turnover products in Escherichia coli. Being a N-acetyl-anhydromuranmyl-L-alanine amidase AmpD is likely to be involved in recycling of the turnover products. It is suggested that the negative regulatory effect of AmpD is due to the hydrolysis of anhydro-muropeptides which may function as signals for beta-lactamase induction.
Relationship between aconitase gene expression and sporulation in Bacillus subtilis (1987)

The citB of Bacillus subtilis codes for aconitase (D. W. Dingman and A. L. Sonenshein, J. Bacteriol. 169:3060-3065). By direct measurements of citB mRNA levels and by measurements of beta-galactosidase activity in a strain carrying a citB-lacZ fusion, we have examined the expression of citB during growth and sporulation. When cells were grown in nutrient broth sporulation medium, citB mRNA appeared in mid- to late-exponential phase and disappeared by the second hour of sporulation. This timing corresponded closely to the kinetics of appearance of aconitase enzyme activity. Decoyinine, a compound that induces sporulation in a defined medium, caused a rapid simultaneous increase in aconitase activity and citB transcription. After decoyinine addition, the rate of increase in aconitase activity in a 2-ketoglutarate dehydrogenase (citK) mutant and in a citrate synthase (citA) mutant was significantly less than in an isogenic wild-type strain. This is apparently due to a failure to deplete 2-ketoglutarate and accumulate citrate. These metabolites might act as negative and positive effectors of citB expression, respectively. Mutations known to block sporulation at an early stage (spo0H and spo0B) had no appreciable effect on citB expression or aconitase activity. These results suggest that appearance of aconitase is stimulated by conditions that induce sporulation but is independent of certain gene products thought to act at an early stage of sporulation.
Removal of Mercuric Ion from Aqueous Solutions Using Sawdust Coated by Polyaniline (2006)

This paper deals with a new application of polyaniline synthesized chemically, coated on sawdust via cast method in the form of emeraldine base (EB) from formic acid as solvent, and used as an effective adsorbent for removal of mercuric ion or other heavy metals from aqueous solution. Among the different parameters investigated, the effect of pH was found to be the most prominent. It was found that metal uptake is occurred under neutral or slightly alkaline conditions, while under relatively strong acidic media, the sorption of the investigated metal ions was negligible and desorption is a predominant process.
Pentoxifylline as an ancillary treatment for severe falciparum malaria in Thailand. (1998)

Pentoxifylline, an inhibitor of tumor necrosis factor, has been evaluated as an antimalarial agent in combination with artesunate in 45 patients with severe falciparum malaria. Patients were admitted to the intensive care unit at the Hospital for Tropical Diseases in Bangkok, Thailand, and randomly assigned to treatment for 72 hr with a combination of intravenously administered artesunate and 1) placebo, 2) low-dose pentoxifylline (0.83 mg/kg/hr), or 3) high-dose pentoxifylline (1.67 mg/kg/hr). All 45 patients had one or more manifestations of severe malaria such as cerebral malaria (n = 18), renal failure requiring hemodialysis (n = 9), azotemia (n = 8), jaundice (n = 25), or hyperparasitemia (n = 30). The overall severity was comparable in the three groups. Clinical outcome was assessed with respect to the parasite clearance time and the fever clearance time in all patients. In addition, a number of subsidiary outcome variables were examined in specific subgroups, including the recovery time from coma for patients with cerebral malaria, the duration of intubation in patients with respiratory distress, the number of hemodialysis treatments needed for patients with acute renal failure, and the number of units of blood administered to patients requiring transfusion. Concentrations of tumor necrosis factor were reduced in all three groups at 48 hr after treatment. No significant differences among the three treatment groups were found for any of the outcome variables examined. We conclude that the addition of pentoxifylline to artesunate therapy for severe malaria produced no evident clinical benefit.
Bone Mineral Density Thresholds for Pharmacological Intervention to Prevent Fractures (2004)

Using peripheral measurement devices, 82% of postmenopausal women with fractures had T scores better than -2.5. A strategy to reduce overall fracture incidence will likely require lifestyle changes and a targeted effort to identify and develop treatment protocols for women with less severe low bone mass who are nonetheless at increased risk for future fractures.
Examination of DNA methylation of chromosomal hot spots associated with breast cancer. (1993)

Widespread hypomethylation of DNA and regional hypermethylation, including tumor suppressor regions, have been demonstrated in several human cancers. Since a highly heterogeneous array of genetic anomalies have been associated with breast cancer, we examined several chromosomal hot spots for abnormal methylation patterns. Low-levels of increased methylation of HRAS (11p15) were observed between normal and tumor breast tissue samples from 8 patients. No noticeable variation in methylation was observed with DNA probes from chromosomes 11p15, 1p36, 17q22, 17p13.3 and 3p21 for the 7 ductal breast carcinoma patients, though some variability was observed for a patient with atypical medullary carcinoma. Additionally, the methylation pattern of the estrogen-receptor gene (6q24-27), whose protein product is increased in numerous breast cancers, also did not change. Therefore, as opposed to other cancer types, widespread hypomethylation and regional hypermethylation do not appear to be involved in the early stages of breast cancer and does not account for the molecular heterogeneity of the disease. Proposed alternative mechanisms for the diversity of genetic alterations associated with breast cancer are discussed.
Color-Based Retrieval Of Facial Images (2000)

Publication in the conference proceedings of EUSIPCO, Tampere, Finland, 2000
Vertically standing carbon nanotubes as charge storage nodes for an ultimately scaled nonvolatile memory application (2007)

Vertically standing single-walled carbon nanotube (SSWCNT)-embedded transistors have been demonstrated for a flash memory application. The performance of the SSWCNT device was compared with a lying SWCNT (LSWCNT) device to verify the directional effect of immobilized SWCNTs. The SSWCNT device shows a better program/erase transient and a threefold enhanced retention characteristics over the LSWCNT device due to the high coupling ratio and the defect immunity based on the isolated distribution and vertical directionality nature of the SSWCNT.
Snoring-related energy transmission to the carotid artery in rabbits (2006)

Epidemiological studies link habitual snoring and stroke, but mechanisms involved are poorly understood. One previously advanced hypothesis is that transmitted snoring vibration energy may promote carotid atheromatous plaque formation or rupture. To test whether vibration energy is present in carotid artery walls during snoring we developed an animal model in which we examined induced snoring (IS)-associated tissue energy levels. In six male, supine, anesthetized, spontaneously breathing New Zealand White rabbits, we surgically inserted pressure transducer-tipped catheters (Millar) to monitor tissue pressure at the carotid artery bifurcation (PCT) and within the carotid sinus lumen (PCS; artery ligated). Snoring was induced via external compression (sandbag) over the pharyngeal region. Data were analyzed using power spectral analysis for frequency bands above and below 50 Hz. For frequencies below 50 Hz, PCT energy was 2.2 (1.1-12.3) cmH2O2 [median (interquartile range)] during tidal breathing (TB) increasing to 39.0 (2.5-95.0) cmH2O2 during IS (P = 0.05, Wilcoxon's signed-rank test). For frequencies > 50 Hz, PCT energy increased from 9.2 (8.3-10.4) x 10(-4) cmH2O2 during TB to 172.0 (118.0-569.0) x 10(-4) cmH2O2 during IS (P = 0.03). Concurrently, PCS energy was 13.4 (8.5-18.0) x 10(-4) cmH2O2 during TB and 151.0 (78.2-278.8) x 10(-4) cmH2O2 during IS (P < 0.03). The PCS energy was greater than PCT energy for the 100-275 Hz bandwidth. In conclusion, during IS there is increased energy around and within the carotid artery, including lower frequency amplification for PCS. These findings may have implications for carotid atherogenesis and/or plaque rupture.
Tumor Necrosis Factor α Stimulates Osteoclast Differentiation by a Mechanism Independent of the Odf/Rankl–Rank Interaction (2000)

Osteoclast differentiation factor (ODF, also called RANKL/TRANCE/OPGL) stimulates the differentiation of osteoclast progenitors of the monocyte/macrophage lineage into osteoclasts in the presence of macrophage colony-stimulating factor (M-CSF, also called CSF-1). When mouse bone marrow cells were cultured with M-CSF, M-CSF-dependent bone marrow macrophages (M-BMM phi) appeared within 3 d. Tartrate-resistant acid phosphatase-positive osteoclasts were also formed when M-BMM phi were further cultured for 3 d with mouse tumor necrosis factor alpha (TNF-alpha) in the presence of M-CSF. Osteoclast formation induced by TNF-alpha was inhibited by the addition of respective antibodies against TNF receptor 1 (TNFR1) or TNFR2, but not by osteoclastogenesis inhibitory factor (OCIF, also called OPG, a decoy receptor of ODF/RANKL), nor the Fab fragment of anti-RANK (ODF/RANKL receptor) antibody. Experiments using M-BMM phi prepared from TNFR1- or TNFR2-deficient mice showed that both TNFR1- and TNFR2-induced signals were important for osteoclast formation induced by TNF-alpha. Osteoclasts induced by TNF-alpha formed resorption pits on dentine slices only in the presence of IL-1alpha. These results demonstrate that TNF-alpha stimulates osteoclast differentiation in the presence of M-CSF through a mechanism independent of the ODF/RANKL-RANK system. TNF-alpha together with IL-1alpha may play an important role in bone resorption of inflammatory bone diseases.
Biochemical properties and immunogenicity of L-phenylalanine ammonia-lyase: effects on tumor-bearing mice. (1979)

L-Phenylalanine ammonia-lyase (PAL) from yeast was used to deplete plasma L-phenylalanine and L-tyrosine in an attempt to achieve inhibition of tumor growth in mice. Plasma L-phenylalanine and L-tyrosine were reduced to nondetectable levels when circulating PAL activity was maintained at greater than or equal to 0.06 unit/ml. Repeated administration resulted in the appearance of anti-PAL antibodies. A radioimmunoassay based on the method of Farr was developed to determine quantitatively the presence of anti-PAL. Sublethal total-body irradiation temporarily suppressed the immunologic response of the host. Long-term specific immunosuppression to PAL was achieved with cyclophosphamide (CPA). A single dose of 180 mg/kg of CPA administered ip to mice 24 hours before, simultaneously with, or 24 hours after 100 units/kg of PAL induced tolerance for 450 days (20 injections of enzyme). The plasma half-life of PAL in CPA-treated mice remained essentially the same as that found after a single injection (25 hours), and anti-PAL probably will require specific immunosuppression of the host to repeated injections of the enzyme.
Texture of Ru columns grown by oblique angle sputter deposition (2006)

Ru films were sputter deposited on native oxide p-Si(100) substrates under normal incidence and oblique angle incidence with and without substrate rotation. We characterized the crystalline texture and morphology of the Ru films by x-ray diffraction, transmission electron microscopy, and scanning electron microscopy. For the case of normal incidence, a smooth, uniform surface layer was observed, and pole figure analysis showed coexisting {101¯0}, {0002}, and {101¯1} normally oriented textures. For oblique angle incidence, we found that the films grown by uniform substrate rotation consist of isolated, vertical columnar structures with a clear pyramidal-shaped apex and display a normal {101¯0} fiber texture. Individual vertical columns were found to possess a single-crystal structure. In comparison, Ru films grown without substrate rotation possess a slanted columnar structure. They mainly show a tilted {101¯1}{101¯0} two-orientation (II-O) texture, with non-negligible {101¯0}{112¯0} and {0002} {112¯0} II-O textures as well. The formation of textures under oblique angle deposition was ascribed to the competition between crystalline planes having different vertical growth rates, where the planes associated with a higher rate survive from the shadowing effects. We argue that the vertical growth rate is determined by the atom mobility. Under substrate rotation this mobility is correlated with the overall atomic roughness of the crystalline planes. For a fixed substrate the adatom mobility exhibits anisotropic behavior, which is reflected in the biased diffusion.
The Nano Processor: a low resource reconfigurable processor (2002)

Reconfigurable logic systems approach the performance of application-specific integrated circuits (ASICs) while retaining much of the generality of conventional computing systems through reconfiguration. Unfortunately, the development of these systems, unlike conventional software systems, is hardware-intensive, requiring significant hardware development time. One way to introduce a more flexible development approach is to implement a customizable stored-program processor. For a given application, the designer can develop customized hardware to increase performance and then control the sequencing and operation of this hardware with software. Development time can be significantly reduced because conventional software development tools, e.g. assemblers and compilers, can be used to quickly develop new applications on the customized processor. This paper presents the Nano Processor, a fully customizable reconfigurable processor, together with its integrated assembler, that has been successfully implemented on the Xilinx 3000 series field programmable gate array (FPGA).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Magneto-optical properties of (BiGdY)3Fe5O12 for optical magnetic field sensors (1994)

The temperature dependent sensitivity characteristic in the zeroth-order diffraction beam from the multidomain materials of BiXGdYY3−(X+Y)Fe5O12 films grown by a conventional liquid-phase-epitaxial method are studied. By measuring the variation of the sensitivity with temperature, it was found that films with X=1.3 and Y=0.43 show the minimum value of ±0.5% between 253 and 353 K. The contribution of the Gd substitution on the improvement of the temperature dependence of the sensitivity was explained by a simple theoretical calculation.
Mutation detection using immobilized mismatch binding protein (MutS) (1995)

An accurate and highly sensitive mutation detection assay has been developed. The assay is based on the detection of mispaired and unpaired bases by immobilized mismatch binding protein (Escherichia coli MutS). The assay can detect most mismatches and all single base substitution mutations, as well as small addition or deletion mutations. The assay is simple to use and does not require the use of either radioactivity or gel electrophoresis.
Heterocyclic compounds. 4. Synthesis and antiinflammatory activity of some substituted thienopyrimidones (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHeterocyclic compounds. 4. Synthesis and antiinflammatory activity of some substituted thienopyrimidonesM. S. Manhas, S. D. Sharma, and S. G. AminCite this: J. Med. Chem. 1972, 15, 1, 106–107Publication Date (Print):January 1, 1972Publication History Published online1 May 2002Published inissue 1 January 1972https://pubs.acs.org/doi/10.1021/jm00271a034https://doi.org/10.1021/jm00271a034research-articleACS PublicationsRequest reuse permissionsArticle Views137Altmetric-Citations35LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Releasable Conjugation of Polymers to Proteins (2015)

Many synthetic strategies are available for preparing well-defined conjugates of peptides/proteins and polymers. Most reports on this topic involve coupling methoxy poly(ethylene glycol) to therapeutic proteins, a process referred to as PEGylation, to increase their circulation lifetime and reduce their immunogenicity. Unfortunately, the major dissuading dogma of PEGylation is that, in many cases, polymer modification leads to significant (or total) loss of activity/function. One approach that is gaining momentum to address this challenge is to release the native protein from the polymer with time in the body (releasable PEGylation). This contribution will present the state-of-the-art of this rapidly evolving field, with emphasis on the chemistry behind the release of the peptide/protein and the means for altering the rate of release in biological fluids. Linkers discussed include those based on the following: substituted maleic anhydride and succinates, disulfides, 1,6-benzyl-elimination, host-guest interactions, bicin, β-elimination, biodegradable polymers, E1cb elimination, β-alanine, photoimmolation, coordination chemistry, zymogen activation, proteolysis, and thioesters.
RHPN2 Drives Mesenchymal Transformation in Malignant Glioma by Triggering RhoA Activation (2013)

Mesenchymal transformation is a hallmark of aggressive glioblastoma (GBM). Here, we report the development of an unbiased method for computational integration of copy number variation, expression, and mutation data from large datasets. Using this method, we identified rhophilin 2 (RHPN2) as a central genetic determinant of the mesenchymal phenotype of human GBM. Notably, amplification of the human RHPN2 gene on chromosome 19 correlates with a dramatic decrease in the survival of patients with glioma. Ectopic expression of RHPN2 in neural stem cells and astrocytes triggered the expression of mesenchymal genes and promoted an invasive phenotype without impacting cell proliferation. Mechanistically, these effects were implemented through RHPN2-mediated activation of RhoA, a master regulator of cell migration and invasion. Our results define RHPN2 amplification as a central genetic determinant of a highly aggressive phenotype that directs the worst clinical outcomes in patients with GBM.
[Synthesis of phosphonate analogs of sphingomyelins and preparation of an affinity sorbent for sphingomyelinase purification]. (1987)

Phosphonate analogues of 2-N-stearoyl- (I) and 2-N-(undec-10-enoyl)-sphingomyelins (II) have been synthesised. Compound (II) was used as a starting product for preparation of a sorbent for sphingomyelinase affinity chromatography. The double bond of the unsaturated undec-10-enoyl moiety of the phosphonate analogue (II) was oxidized, and the modified (II) was coupled to amino-Toyopearl HW-65 to give a sorbent containing 4 mumoles of ligand per milliliter of the swollen resin.
Identification of the Envelope V3 Loop as the Primary Determinant of Cell Tropism in HIV-1 (1991)

Cells of the monocyte-macrophage lineage are targets for human immunodeficiency virus-1 (HIV-1) infection in vivo. However, many laboratory strains of HIV-1 that efficiently infect transformed T cell lines replicate poorly in macrophages. A 20-amino acid sequence from the macrophage-tropic BaL isolate of HIV-1 was sufficient to confer macrophage tropism on HTLV-IIIB, a T cell line--tropic isolate. This small sequence element is in the V3 loop, the envelope domain that is the principal neutralizing determinant of HIV-1. Thus, the V3 loop not only serves as a target of the host immune response but is also pivotal in determining HIV-1 tissue tropism.
Possible implementation of adiabatic quantum algorithm with superconducting flux qubits (2005)

We show that an $LC$ parametric transducer can be effectively used to monitor an adiabatic evolution of the superconducting flux qubit. We propose a scheme to measure the qubit's state, which is a quantum nondemolition measurement. The scheme can be easily extended to a three-qubit system and allows the reading out of the qubits' states while the system remains in the ground state. An implementation of the adiabatic quantum algorithm MAXCUT for three superconducting flux qubits is discussed.
Electrochemical Properties of Small Carbon Nano-Onion Films (2010)

The electrochemical properties of small carbon nano-onions (CNOs) in the solid phase, nonmodified carbon nano-onions (n-CNOs), and CNOs functionalized with carboxylic acid groups [oxidized carbon nano-onions (ox-CNOs)] were investigated by cyclic voltammetry. The redox properties of CNO films depend on the functionalization of the carbon surface. In aqueous solutions, the n-CNO/tetra(-octyl)ammonium bromide (TOABr) films show a behavior typical of an ideal double-layer capacitor with a specific capacitance close to . The ox-CNOs are electrochemically active at negative potentials due to carboxylic group reduction. Modification of the nano-onion surface with carboxylic groups results in a decrease in the specific capacitance of ox-CNO/TOABr films to .