gebhart/patrepeval huggingface dataset:
Conversion of the Bifunctional 8-Oxoguanine/β-δ Apurinic/Apyrimidinic DNA Repair Activities ofDrosophila Ribosomal Protein S3 into the Human S3 Monofunctional β-Elimination Catalyst through a Single Amino Acid Change (2001)

The Drosophila S3 ribosomal protein has important roles in both protein translation and DNA repair. In regards to the latter activity, it has been shown that S3 contains vigorous N-glycosylase activity for the removal of 8-oxoguanine residues in DNA that leaves baseless sites in their places. Drosophila S3 also possesses an apurinic/apyrimidinic (AP) lyase activity in which the enzyme catalyzes a beta-elimination reaction that cleaves phosphodiester bonds 3' and adjacent to an AP lesion in DNA. In certain situations, this is followed by a delta-elimination reaction that ultimately leads to the formation of a single nucleotide gap in DNA bordered by 5'- and 3'-phosphate groups. The human S3 protein, although 80% identical to its Drosophila homolog and shorter by only two amino acids, has only marginal N-glycosylase activity. Its lyase activity only cleaves AP DNA by a beta-elimination reaction, thus further distinguishing itself from the Drosophila S3 protein in lacking a delta-elimination activity. Using a hidden Markov model analysis based on the crystal structures of several DNA repair proteins, the enzymatic differences between Drosophila and human S3 were suggested by the absence of a conserved glutamine residue in human S3 that usually resides at the cleft of the deduced active site pocket of DNA glycosylases. Here we show that the replacement of the Drosophila glutamine by an alanine residue leads to the complete loss of glycosylase activity. Unexpectedly, the delta-elimination reaction at AP sites was also abrogated by a change in the Drosophila glutamine residue. Thus, a single amino acid change converted the Drosophila activity into one that is similar to that possessed by the human S3 protein. In support of this were experiments executed in vivo that showed that human S3 and the Drosophila site-directed glutamine-changed S3 performed poorly when compared with Drosophila wild-type S3 and its ability to protect a bacterial mutant from the harmful effects of DNA-damaging agents.
Role of the Histone Acetyl Transferase Tip60 in the p53 Pathway (2004)

The histone acetyl transferase Tip60 (HTATIP) shares many properties with the tumor suppressor p53 (TP53). Both proteins are involved in the cellular response to DNA damage, are subjected to proteasomal digestion following Mdm2-mediated ubiquitination, and accumulate after UV irradiation. We found here that knock-down of Tip60 affects the p53-dependent response following actinomycin D treatment, most likely because it inhibits p21 (CDKN1A) accumulation. Moreover, Tip60 is required for p53 to activate the endogenous p21 promoter, suggesting that it functions as a p53 co-activator. However, we also found that knock-down of Tip60 increases the turnover rate of p53 under normal growth conditions. Tip60 interferes with Mdm2-mediated degradation of p53, probably because it affects its subcellular localization. Taken together, our results suggest that Tip60 plays a double role in the p53 pathway: under normal growth conditions, Tip60 contributes to maintain a basal pool of p53 by interfering with its degradation; following DNA damage, Tip60 functions as p53 co-activator. That these two distinct roles are linked during the p53-dependent response is an attractive hypothesis.
Freeman ion source: An overview (invited) (1992)

The Freeman ion source has now been in use for some 30 years. It is still the most versatile and most widely used ion source. Its ability to produce sharply focused milliampere beams of most elements over a wide range of energies continue to make it a popular choice of ion source. For use in semiconductor ion implanters its performance and relative ease of operation has led to it being extensively used for the production doping of silicon devices. Over the years the Freeman ion source has also been very successfully used in many other fields of ion implantation, including the routine production of multimilliampere beams of a wide range of metallic ions. The production of ion beams will be discussed in detail. Issues such as filament lifetime will also be covered. Recent developments and possible future innovations will be mentioned.
The Pericardium Reinforced Suture Annuloplasty: Another Tool Available for Mitral Annulus Repair? (1993)

From May 1985 to May 1992, 169 patients underwent surgery for mitral valve repair. In 87% of these patients, the valve reconstruction involved the mitral annulus. At the beginning, in an effort to preserve systolic movement of the annulus and avoid the implant of prosthetic materials inside the heart, we mainly used simple suture annuloplasty in 66 patients. When we reoperated upon three patients only a few months after reconstruction of the mitral valve for a dehiscence of the suture annuloplasty, we decided to perform ring annuloplasty with the Carpentier ring in 23 patients. Though we have not seen any problems with the Carpentier ring in our series, we performed a suture annuloplasty reinforced with a strip of autologous pericardium to eliminate all prosthetic material. Since introducing this technique in 1989, we have used this annuloplasty in 58 patients. We have not observed any dehiscence of the suture or other complications related to this procedure. Three patients with a pericardial annuloplasty underwent reoperation for other reasons; the autologous pericardium was perfectly attached to the annulus, covered by a smooth layer of fibrous tissue without calcification. After this encouraging initial experience, we believe that long-term follow-up is necessary to confirm that autologous pericardium is an effective method of mitral annulus repair.
Strain induced giant magnetism in epitaxial Fe16N2 thin film (2013)

We report a direct observation of giant saturation magnetization in Fe16N2. By exploiting thin film epitaxy, which provides controlled biaxial stress to create lattice distortion, we demonstrate that giant magnetism can be established in Fe16N2 thin film coherently grown on MgO (001) substrate. Explored by polarized neutron reflectometry, the depth-dependent saturation magnetic induction (Bs) of epitaxial Fe16N2 thin films is visualized, which reveals a strong correlation with the in-plane lattice parameter and tensile strain developed at near substrate interface. With controlled growth process and dimension adjustment, the Bs of these films can be modulated over a broad range, from ∼2.1 Tesla (T) (normal Bs) up to ∼3.1 T (giant Bs).
Antisense oligodeoxyribonucleotide as to the growth factor midkine suppresses neointima formation induced by balloon injury (2005)

Restenosis is the major clinical problem of angioplasty. We have previously shown that neointima formation is strikingly suppressed in midkine (MK)-deficient mice. Neointima formation is restored if MK protein is administrated to the deficient mice. MK is a heparin-binding growth factor and implicated in the migration of inflammatory cells and vascular smooth muscle cells. Consistently, the suppression of neointima formation in the deficient mice is accompanied by suppression of recruitment of inflammatory cells into the vascular wall. Here, we evaluated the potential of MK antisense oligodeoxyribonucleotide (ODN) for the prevention of restenosis. We cloned the cDNA of rabbit MK, which showed a strongly conserved sequence in mammals. The balloon injury induced MK expression, with the maximum level occurring 7-14 days after angioplasty, in the rabbit carotid artery. Two antisense ODNs suppressed the production of MK in a rabbit kidney cell line, RK13 cells, one of which was then transfected into the arterial wall by means of lipofection immediately after balloon treatment. The antisense ODN suppressed MK induction in vivo and consequently suppressed neointima formation to 60% of the control level. These results suggest that MK is a candidate molecular target for the therapy for vascular restenosis.
The performance of an integrated air purifier for control of aerosol, microbial, and odor (1993)

A new type of an air purifier has been developed for a simultaneous control of aerosol, microbial, and odor in living environments using ozone, corona precharger, an electrified minipleats filter, and an ozone-decomposing catalyzer as well as a semiconductor ozone sensor for safety control. Ozone is generated in the corona precharger by enhancing negative corona with the application of a higher-than-ordinary voltage. This device, which is named AIP, indicates 85% one-through number collection efficiency for aerosol particles in the size range of 0.1-1.0 mm. AIP shows a very satisfactory deodorizing performance for man-originated and living environment-originated odors, such as ammonia, hydrogen sulfide,methylmercaptane, etc. The AIP also effectively kills, through long exposure to low-concentration ozone, most bacteria, fungi, viruses, and other microbials and small insects collected in its filter.
Evaluation of polysaccharides intended for ophthalmic use in ocular dosage forms. (1995)

Different water-soluble polysaccharides were evaluated for their intended use in ocular dosage forms. The physicochemical characteristics and the viscosity of the solutions prepared with several iso-osmotic vehicles were measured. The influence of ions present in lacrimal fluid, mucin and cyclodextrin on the rheological behaviour was examined. Scleroglucan and xanthan gum exhibit viscoelastic and mucoadhesive properties useful for ocular dosage form formulations.
Adiabatic theory of outer sphere electron-transfer reactions in solution (1961)

The first page of this article is displayed as the abstract.
Sequence Specific Thermodynamic and Structural Properties for DNA.cntdot.RNA Duplexes (1994)

DNA.RNA hybrid duplexes are found in many important biological processes and are involved in developing modes of disease treatment, such as antisense therapy, yet little is known about the sequence dependence of their structure and stability. The structure and thermodynamic stability of DNA.RNA hybrid model systems corresponding in composition and length and containing (1) all purine or all pyrimidine bases on each strand or (2) mixed purine and pyrimidine bases on each strand have been evaluated relative to pure RNA and DNA duplexes by thermal melting, CD, and electrophoresis analyses. The spread in free energies of denaturation of the homopurine.homopyrimidine systems covers over 14 kcal/mol of single strands, while the mixed sequence free energies vary by less than 4 kcal/mol. The RNA-homopurine.DNA-homopyrimidine hybrid resembles a corresponding pure RNA duplex in both structure and stability, whereas the DNA-homopurine.RNA-homopyrimidine hybrid resembles a corresponding pure DNA duplex. The mixed sequence hybrids show intermediate structure between the corresponding pure RNA and pure DNA duplexes and a stability closer to that of the pure DNA duplex. From these results and the evaluation of published hybrid data [Hall, K. B., & McLaughlin, L. W. (1991) Biochemistry 30, 10606-10613; Roberts, W. R., & Crothers, D. M. (1992) Science 258, 1463-1466], it can be predicted that a hybrid duplex containing more RNA purine bases will have a CD spectrum, and probably conformation, resembling that of A-form duplexes and will be more stable than a corresponding hybrid duplex with fewer RNA purine bases.
An Improved Method of Preparing Diethylgermanium Derivatives (1933)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn Improved Method of Preparing Diethylgermanium DerivativesL. Horvitz and E. A. FloodCite this: J. Am. Chem. Soc. 1933, 55, 12, 5055Publication Date (Print):December 1, 1933Publication History Published online1 May 2002Published inissue 1 December 1933https://doi.org/10.1021/ja01339a506RIGHTS & PERMISSIONSArticle Views34Altmetric-Citations6LEARN 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 InReddit PDF (94 KB) Get e-Alerts Get e-Alerts
First Principles of Typography (1951)

Journal Article First Principles of Typography Get access Notes and Queries, Volume CXCVI, Issue jul07, 7 July 1951, Page 308, https://doi.org/10.1093/nq/CXCVI.jul07.308a Published: 07 July 1951
A transforming growth factor beta-like immunosuppressive factor in immunoglobulin G-binding factor. (1995)

Immunoglobulin G-binding factors (IgG-BF), which are produced by cells of the immune system, inhibit antibody production. In this paper, we show that transforming growth factor-beta (TGF-beta) suppresses secondary in vitro anti-sheep red blood cell responses of mouse splenocytes and lipopolysaccharide- or anti-IgM-stimulated mouse B cell responses in a way similar to, and with the same kinetics as, rodent IgG-BF. Moreover, the immunosuppressive activity of IgG-BF was totally neutralized by polyclonal and monoclonal anti-TGF-beta antibodies and it eluted with TGF-beta by gel exclusion chromatography, suggesting that a TGF-beta-like immunosuppressive factor is present in IgG-BF. We also show that TGF-beta behaves as an IgG-BF since it binds to insolubilized IgG, but not to insolubilized F(ab')2 or bovine serum albumin. Altogether, the data support the concept of a biological role for TGF-beta in the IgG-mediated negative feedback of antibody responses.
Transcriptional Regulation by Heavy Metals, Exemplified at the Metallothionein Genes (1995)

Seventeen of the thirty elements known to be essential for life are metals (Cotton and Wilkinson, 1980). They can function as structural or catalytic components of bioorganic molecules or even as signal transducers. (Lippard, 1993). The so-called transition metals are found in the groups HIB to IIB of the periodic system. Of these, zinc (Group IIB) is the most widely used in living systems. In 1869 it was discovered that zinc is an essential trace element for higher organisms, and in 1940, it was the first trace element to be recognized as a component of an enzyme, namely carbonic anhydrase (Raulin, 1869; Keilin and Mann, 1940). To date, there are more than 300 enzymes known to require zinc for proper functioning (Vallee and Auld, 1990). Pathological zinc deficiency, due to greatly reduced intestinal zinc uptake as in the recessive, autosomal disorder Acrodermatitis enteropathica, leads to death unless treated by high oral zinc doses (Vallee and Falchuk, 1993). Among the zinc dependent enzymes several are involved in nucleic acid metabolism such as the prokaryotic and eukaryotic RNA polymerases (Vallee and Falchuk, 1993). It has been discovered only recently that zinc is also an integral constituent of proteins that regulate the activity of eukaryotic RNA polymerases.
NLRP3 Inflammasome: The Stormy Link Between Obesity and COVID-19 (2020)

Several countries around the world have faced an important obesity challenge for the past four decades as the result of an obesogenic environment. This disease has a multifactorial origin and it is associated with multiple comorbidities including type 2 diabetes, hypertension, osteoarthritis, metabolic syndrome, cancer, and dyslipidemia. With regard to dyslipidemia, hypertriglyceridemia is a well-known activator of the NLRP3 inflammasome, triggering adipokines and cytokines secretion which in addition induce a systemic inflammatory state that provides an adequate scenario for infections, particularly those mediated by viruses such as HIV, H1N1 influenza, and SARS-CoV-2. The SARS-CoV-2 infection causes the coronavirus disease 2019 (COVID-19) and it is responsible for the pandemic that we are currently living. COVID-19 causes an aggressive immune response known as cytokine release syndrome or cytokine storm that causes multiorgan failure and in most cases leads to death. In the present work, we aimed to review the molecular mechanisms by which obesity-associated systemic inflammation could cause a more severe clinical presentation of COVID-19. The SARS-CoV-2 infection could potentiate or accelerate the pre-existing systemic inflammatory state of individuals with obesity, <i>via</i> the NLRP3 inflammasome activation and the release of pro-inflammatory cytokines from cells trough Gasdermin-pores commonly found in cell death by pyroptosis.
The practical application of reflectance spectrophotometry for the demonstration of haemoglobin and its degradation in bruises (2004)

The ability to demonstrate the presence of haemoglobin and measure its degradation in bruises in living human subjects by a non-invasive method has not been described previously, and may be of use in the objective ageing of bruises for forensic purposes.
Statistical Analysis between Output and Energy Consumption of Production Process in Iron and Steel Industry (2017)

On the basis of E-P theory of cleaner production, this paper verifies its reliability in terms of prediction of energy consumption using actual production data of output and energy consumption. And then the parameters of the E-P model are determinate by means of least square linear programming method. In addition, we use the actual data to further modify the E-P model in order to improve accuracy of model. It is proved that this model can forecast energy consumption kindly.
Inexact match associative memory cell (1991)

A new associative memory cell is described and analysed using SPICE3d1. The CMOS cell uses current summation to compute, in parallel, Hamming distances between the search key and each word in the memory. For 32 bit words, SPICE simulations of a 2μm process show a delay of 4ns/bit for Hamming distances less than three.
Molecular actions of smoking cessation drugs at α4β2 nicotinic receptors defined in crystal structures of a homologous binding protein (2012)

Partial agonists of the α4β2 nicotinic acetylcholine receptor (nAChR), such as varenicline, are therapeutically used in smoking cessation treatment. These drugs derive their therapeutic effect from fundamental molecular actions, which are to desensitize α4β2 nAChRs and induce channel opening with higher affinity, but lower efficacy than a full agonist at equal receptor occupancy. Here, we report X-ray crystal structures of a unique acetylcholine binding protein (AChBP) from the annelid Capitella teleta, Ct-AChBP, in complex with varenicline or lobeline, which are both partial agonists. These structures highlight the architecture for molecular recognition of these ligands, indicating the contact residues that potentially mediate their molecular actions in α4β2 nAChRs. We then used structure-guided mutagenesis and electrophysiological recordings to pinpoint crucial interactions of varenicline with residues on the complementary face of the binding site in α4β2 nAChRs. We observe that residues in loops D and E are molecular determinants of desensitization and channel opening with limited efficacy by the partial agonist varenicline. Together, this study analyzes molecular recognition of smoking cessation drugs by nAChRs in a structural context.
Knowledge-based automatic detection of multitype lung nodules from multidetector CT studies (2002)

Multi-slice computed tomography (CT) provides a promising technology for lung cancer detection and treatment. To optimize automatic detections of a more complete spectrum of lung nodules on CT requires multiple specialized algorithms in a coherently integrated detection system. We have developed a knowledge-based system for automatic lung nodule detection and analysis, which coherently integrates several robust novel detection algorithms to detect different types of nodules, including those attached to the chest wall, nodules adjacent to or fed by vessels, and solitary nodules, simultaneously. The system architecture can be easily extended in the future to include a still greater range of nodule types, most importantly so-called ground-glass opacities (GGOs). In addition, automatic local adaptive histogram analysis, dynamic cross-correlation analysis, and the automatic volume projection analysis by using by data dimension reduction method, are used in nodule detection. The proposed system has been applied to 10 patients screened with low-dose multi-slice CT. Preliminary clinical tests show that (1) the false positive rate averages about 3.2 per study; and (2) by using the system radiologists are able to detect nearly twice the number of nodules as compared with working alone.
Boundary Waters Canoe Area - Quetico Provincial Park: an international partnership. (1984)

Advanced CMR imaging ensures more detailed tissue characterization in patients with chronic MI without a relevant increase in imaging and post-processing time. Fatty metaplasia may influence regional myocardial deformation especially in the myocardial segments adjacent to scar tissue. A simplified and shortened myocardial viability CMR protocol might be useful to better characterize and stratify patients with chronic MI.
Altered ion transport by tracheal glands in cystic fibrosis (1991)

Acini of tracheal glands from 12 humans without cystic fibrosis (CF) and from two CF patients were isolated by enzymatic digestion. They were plated on flasks coated with human placental collagen (HPC) in media containing Ultroser G serum substitute and a variety of growth factors. Confluent cell sheets formed after 20 days. Cells were then isolated by trypsinization and replated at 10(6) cells/cm2 onto porous-bottomed inserts coated with HPC. Confluent sheets formed on day 1 after replating and were studied on day 10 in Ussing chambers. Transepithelial resistance (Rte) and baseline short-circuit current (Isc) of CF cultures (171 +/- 67 omega.cm2, 3.8 +/- 0.8 microA/cm2; n = 5) were significantly less than non-CF (541 +/- 116 omega.cm2, 9.9 +/- 2.3 microA/cm2; n = 14). Responses in Isc to mediators were also significantly reduced in CF: isoproterenol (10(-5)M) = 0.04 +/- 0.04 vs. 1.9 +/- 0.6; methacholine (10(-5)M) = 0.2 +/- 0.1 vs. 7.1 +/- 1.7; bradykinin (10(-6)M) = 0.4 +/- 0.1 vs. 5.0 +/- 1.0 microA/cm2; n = 5 for CF, n = 14 for non-CF. When CF and non-CF cells were matched for baseline Isc and Rte, the responses of CF cells to mediators still remained statistically lower than normal. The reduced responses of CF cells to bradykinin and methacholine, in addition to isoproterenol, suggest that both Ca-dependent and adenosine 3',5'-cyclic monophosphate-dependent regulation of Cl secretion are defective in CF tracheobronchial glands. The resulting reduction in fluid secretion by glands may contribute to the accumulation of airway mucus in CF.