gebhart/patrepeval huggingface dataset:
Copper-ion-dependent damage to the bases in DNA in the presence of hydrogen peroxide (1991)

Mixtures of Cu2+ and H2O2 at pH 7.4 caused damage to the bases in DNA greater than that caused by mixtures of Fe3+ and H2O2. Addition of ascorbic acid to the Cu2+/H2O2 system caused a very large increase in base damage, much greater than that produced by the Fe3+/H2O2/ascorbic acid system. The products of base damage in the presence of Cu2+ were typical products that have been shown to result from attack of hydroxyl radicals upon the DNA bases. Cytosine glycol, thymine glycol, 8-hydroxyadenine and especially 8-hydroxyguanine were the major products in both the Cu2+/H2O2 and the Cu2+/H2O2/ascorbic acid systems. Base damage in DNA by these systems was inhibited by the chelating agents EDTA and nitrilotriacetic acid and by catalase, but not by superoxide dismutase, nor by the hydroxyl-radical scavenger mannitol. It is proposed that Cu2+ ions bound to the DNA react with H2O2 and ascorbic acid to generate hydroxyl radicals, which then immediately attack the DNA bases in a site-specific manner. A hypoxanthine/xanthine oxidase system also caused damage to the DNA bases in the presence of Cu2+ ions. This was inhibited by superoxide dismutase and catalase. The high activity of Cu2+ ions, when compared with Fe3- ions, in causing hydroxyl-radical-dependent damage to DNA and to other biomolecules, means that the availability of Cu2+ ions in vivo must be carefully controlled.
Rosuvastatin protects against podocyte apoptosis in vitro (2008)

Rosuvastatin is prosurvival in injured podocytes. Rosuvastatin exerts its protective effect through a p21-dependent antiapoptotic pathway. These findings suggest that statins decrease proteinuria by protecting against podocyte apoptosis and subsequent podocyte depopulation.
An Extension of the UEHL Distribution Based on the DUS Transformation (2023)

In this study, we propose a new distribution based on the Dinesh, Umesh, and Sanjay (DUS) transformation by using the Unit Exponentiated Half-Logistic (UEHL) distribution as the baseline distribution, a member of the family of proportional hazard rate models. Moreover, we study several properties, such as moments, skewness, kurtosis, stress-strength reliability, and likelihood ratio ordering. Further, we discuss the statistical inference on the parameters of the proposed distribution by the maximum likelihood estimation (MLE) method. Besides, we conduct a simulation based on the new distribution to investigate the behavior of the maximum likelihood estimates in various conditions. Furthermore, we present a numerical example to show the performance of the distribution on a real-life data set. Finally, we discuss the need for further research.
Multifunctional Monolayer Assemblies for Reversible Direct Fluorescence Transduction of Protein−Ligand Interactions at Surfaces (1999)

This paper describes a convenient new method for preparing functionalizable protein-resistant monolayers that can be used to incorporate ligands and protein-sensitive fluorescent reporter groups, and the use of these monolayers for the detection of protein−ligand interactions. BODIPY X-650/665, a diode laser compatible fluorophore, and biotin, a model ligand, have been used to transduce biospecific interactions between proteins and biotin at surfaces. Silicon wafers or quartz slides were coated with (3-aminopropyl)triethoxysilane, and treated with glutaraldehyde and then 2,2‘-(ethylenedioxy)bis(ethylenediamine). The resultant surface layers are resistant to nonspecific protein adsorption and contain primary amine groups that are available for subsequent derivatization. Chemical modification of the amine-terminated monolayers thus obtained was accomplished using the N-hydroxysuccinimide active ester of BODIPY X-650/665 and biotin activated with Woodward's reagent K. Surfaces treated only with the BODIPY dye for long periods of time to produce a near monolayer coverage of the fluorophore exhibited a dramatic attenuation of the emission of the fluore upon nonspecific adsorption of protein (e.g., albumin). Nonspecific adsorption of proteins can be minimized by diluting the fluore on the surface. Incorporation of a biospecific ligand (i.e., biotin) and the BODIPY fluore in mixed monolayers by serial chemical modification of amine-terminated monolayers yielded surfaces that can be used for fluorescence transduction of biospecific protein adsorption. Specific binding of streptavidin and anti-biotin was detected by a decrease in both the intensity and excited-state lifetime of the fluorescence of the BODIPY dye. Binding of anti-biotin to these surfaces is reversible. No significant change in the intensity was observed upon exposure of these surfaces to solutions of biotin-blocked streptavidin and anti-human IgG. Only a slight change in intensity was observed upon exposure to bovine serum albumin. Phase angle measurements obtained at a single frequency (100 MHz) were used to detect the reversible binding of anti-biotin at the monolayer surface. These observations indicate that it is possible to construct architectures containing ligands and fluores that can be used to detect binding events using lifetime-based measurements. These assemblies should be generalizable to study a wide variety of protein− and cell−surface interactions in biotechnological applications.
Improving CdS quantum-dot materials by the sol-gel method (1994)

In this paper we discuss our approaches and results for the preparation of improved semiconductor quantum dot materials by the sol-gel method. By taking advantage of the low- temperature sol-gel route, the nanostructure and optical properties of CdS quantum dots were greatly improved for device applications. Pore-free sodium borosilicate (NBS) glasses and organically modified silicates (ORMOSILs) were used as matrices for the CdS nanocrystallites. Results from both degenerate four-wave mixing and pump-probe techniques indicated large third-order nonlinear responses of the order of 10<SUP>-6</SUP> esu from CdS-doped NBS glasses. By using potassium ion exchange, the first CdS-doped channel waveguides were fabricated in NBS glasses. Propagation of femtosecond laser pulses through the waveguide was investigated. Pulse breakup effect that may be the result of soliton formation was observed in these waveguides. Polydimethylsiloxane (PDMS) was uses as the organic component to modify the silica gel. CdS-doped ORMOSILs derived from the PDMS- TEOS system exhibits improved mechanical property and film-forming ability compared to purely inorganic gels. Both CdS-doped PDMS-TEOS ORMOSILs and NBS glasses were much more resistant to photodarkening than the glasses made by melting. The use of the bifunctional ligand 3-aminopropyltriethoxysilane (APTES) significantly reduced the average particle size and narrowed the size distribution of CdS quantum dots in silica gels and densified NBS glasses.
Papanicolaou smears in human immunodeficiency virus-seropositive women during follow-up (1995)

Although the long-term outcome of SIL in this population remains unknown, our results emphasize the high rate of persistence of SIL and the relative inefficiency of conventional treatment in HIV-infected women. These findings contrast with the natural history of SIL in immunocompetent women.
The effectiveness of in‐plant chlorination in poultry processing (1975)

1. Sampling carcasses after plucking or after the post-evisceration spray-wash showed that 10 or 20 ppm available chlorine in the processing-plant water supply caused little reduction in carcass contamination. 2. When 20 ppm chlorine was used in the water supply to parts of the processing-plant other than the mechanical immersion chilling system, counts of faecal and spoilage bacteria from carcasses were reduced approximately 10-fold after passage through the chilling system; bacterial carry-over of chlorine from the final spray-washer. 3. Artificial contamination of carcasses with a readily identifiable strain of Escherichia coli confirmed the occurrence of cross-contamination during plucking and evisceration; in-plant chlorination reduced neither the proportion of carasses contaminated nor the numbers of organisms transferred at these stages. 4. In most cases the chlorine-resistance of poultry spoilage pseudomonads was greater than that of E. coli; hence in-plant chlorination is to be recommended for processing-plant water supplies which carry such spoilage organisms.
Effects of age, sex, and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease. A meta-analysis. APOE and Alzheimer Disease Meta Analysis Consortium (1997)

To examine more closely the association between apolipoprotein E (APOE) genotype and Alzheimer disease (AD) by age and sex in populations of various ethnic and racial denominations.Forty research teams contributed data on APOE genotype, sex, age at disease onset, and ethnic background for 5930 patients who met criteria for probable or definite AD and 8607 controls without dementia who were recruited from clinical, community, and brain bank sources.Odds ratios (ORs) and 95% confidence intervals (CIs) for AD, adjusted for age and study and stratified by major ethnic group (Caucasian, African American, Hispanic, and Japanese) and source, were computed for APOE genotypes epsilon2/epsilon2, epsilon2/epsilon3, epsilon2/epsilon4, epsilon3/epsilon4, and epsilon4/epsilon4 relative to the epsilon3/epsilon3 group. The influence of age and sex on the OR for each genotype was assessed using logistic regression procedures.Among Caucasian subjects from clinic- or autopsy-based studies, the risk of AD was significantly increased for people with genotypes epsilon2/epsilon4 (OR=2.6, 95% CI=1.6-4.0), epsilon3/epsilon4 (OR=3.2, 95% CI=2.8-3.8), and epsilon4/epsilon4 (OR=14.9, 95% CI= 10.8-20.6); whereas, the ORs were decreased for people with genotypes epsilon2/epsilon2 (OR=0.6, 95% CI=0.2-2.0) and epsilon2/epsilon3 (OR=0.6, 95% CI=0.5-0.8). The APOE epsilon4-AD association was weaker among African Americans and Hispanics, but there was significant heterogeneity in ORs among studies of African Americans (P<.03). The APOE epsilon4-AD association in Japanese subjects was stronger than in Caucasian subjects (epsilon3/epsilon4: OR=5.6, 95% CI=3.9-8.0; epsilon4/epsilon4: OR=33.1, 95% CI=13.6-80.5). The epsilon2/epsilon3 genotype appears equally protective across ethnic groups. We also found that among Caucasians, APOE genotype distributions are similar in groups of patients with AD whose diagnoses were determined clinically or by autopsy. In addition, we found that the APOE epsilon4 effect is evident at all ages between 40 and 90 years but diminishes after age 70 years and that the risk of AD associated with a given genotype varies with sex.The APOE epsilon4 allele represents a major risk factor for AD in all ethnic groups studied, across all ages between 40 and 90 years, and in both men and women. The association between APOE epsilon4 and AD in African Americans requires clarification, and the attenuated effect of APOE epsilon4 in Hispanics should be investigated further.
Selection and Characterization of RNA Interference-Deficient Trypanosomes Impaired in Target mRNA Degradation (2004)

Genetic analysis of the RNA interference (RNAi) pathway in Trypanosoma brucei has so far revealed one essential component, namely, TbAGO1, encoding a member of the Argonaute protein family. To gain further insight into the RNAi mechanism and its biological significance, we selected RNAi-deficient trypanosomes by using repeated cycles of electroporation with alpha-tubulin double-stranded RNA, a treatment that blocks cytokinesis in wild-type cells. Two independent clones, termed RiD-1 (for RNAi-deficient clone 1) and RiD-2, were characterized. At the cellular level, only RiD-1 trypanosomes showed a significant increase in doubling time with the concomitant accumulation of cells defective in the completion of cytokinesis. At the RNA level, both clones accumulated wild-type amounts of small interfering RNAs and displayed elevated levels of retroposon transcripts, the hallmark of RNAi deficiency in T. brucei. Importantly, both RiD-1 and RiD-2 clones were defective in the degradation of target mRNA, suggesting an impairment of the activity of AGO1, the putative RNAi endonuclease. Since in RiD cells the AGO1 gene was not mutated and was expressed at wild-type levels, we propose that in trypanosomes the cleavage of mRNA by AGO1 is regulated by the interaction with another factor(s).
Catalytic Properties of the SV40 Large T Antigen (1980)

Is the SV40 large tumor (T) antigen an enzyme as well as a specific DNA-binding protein (DBP)? Our current knowledge concerning the structure and function of the SV40 gene-A product encouraged us to ponder such a possibility. We have learned that the gene-A sequences of SV40 encode a large 19S mRNA, which is derived from a transcript containing noncoding intervening sequences (IVS) that are most likely spliced out to form the mature mRNA (Aloni et al. 1977; Berk and Sharp 1978). The translational product of the mature 19S mRNA is a polypeptide with an apparent molecular weight of 90,000–100,000, which can be detected in a phosphorylated state (Tegtmeyer et al. 1977). Under nondenaturing conditions, T antigen has a tendency to form isologous dimers and tetramers as well as heterologous oligomers (Osborn and Weber 1975a; P. Tegtmeyer, pers. comm.; R. Tjian, unpubl.).
Cytotypic differences in the protein composition of the axonally transported cytoskeleton in mammalian neurons (1987)

Many of the structural and functional differences between axons are thought to reflect underlying differences in the biochemical composition and dynamic aspects of the axonal cytoskeleton and cytomatrix. In this study we investigated how the composition of the 2 slow components of axonal transport, SCa and SCb, which convey the cytoskeleton and cytomatrix, differs in axons that are structurally and functionally distinct. For this comparison we analyzed axons of retinal ganglion cells in the optic nerve (ON), axons of dorsal root ganglion (DRG) cells, and axons of ventral motor neurons (VMN) in adult rats. 35S-Methionine-labeled proteins transported with the peak of SCa and SCb were analyzed using high-resolution 2-dimensional polyacrylamide gels (2D-PAGE) and fluorography, and the amounts of major SCa and SCb proteins were quantified. The polypeptide composition of both SCa and SCb was found to be largely similar in DRG and VMN axons, but major qualitative as well as quantitative differences between these axons and ON axons were found. Notable among these were higher ratios of neurofilament protein to tubulin in SCa in DRG and VMN axons compared to ON axons, and significantly larger amounts of 2 microtubule-associated proteins relative to tubulin in SCa of ON axons than in both VMN and DRG axons. Tubulin was the major SCb protein in VMN and DRG axons, but it was not present in SCb in ON axons. Additionally, relatively larger amounts of 2 metabolic enzymes, creatine phosphokinase and nerve-specific enolase, were present in SCb in ON axons than in DRG or VMN axons. The results indicate that significant biochemical heterogeneity among different types of axons can be identified by examining the slow components of axonal transport.
Daily Oral Miltefosine (Hexadecyl-Phosphocholine) in Patients with Advanced Non-Small Cell Lung Cancer. A Phase II Study (1992)

A clinical phase II trial with an oral formulation of miltefosine (MIL) was performed in patients with non-small cell lung cancer (NSCLC). Eligibility criteria for this phase II study included histological proof of NSCLC, measurable locally advanced or metastatic disease without previous radiotherapy of the indicator lesions, no chemotherapy for the diagnosis of cancer prior to entry into the study, WHO performance status of grade < 2, and informed consent. The capsulated drug was given twice daily at a single dose of 50 mg for the first week with the option of increasing the daily dose to 150 mg (50 mg×3) in the second week if tolerability was good. The minimum intended treatment duration was 9 weeks. Twenty-six patients have been entered into the study and 25 are evaluable for toxicity (WHO criteria). Twenty-one patients are evaluable for toxicity and response (WHO criteria). There was 1 PR and 3 patients had a NC of their disease with a duration exceeding twice the period of time for which progression was documented prior to entry into this study (criteria of the AIO phase I/II-study group). Progressive disease was observed in 17 patients with 3 early deaths. Severe side effects were seen in the gastrointestinal tract as abdominal pain, loss of appetite, nausea and vomiting (up to grade 4, WHO) or diarrhea (up to grade 2, WHO). In conclusion, oral MIL given daily showed no major therapeutic activity in patients with NSCLC.
Bis(o-nitrophenyl)ethanediol:  A Practical Photolabile Protecting Group for Ketones and Aldehydes (2002)

The ketals of bis(o-nitrophenyl)ethanediol and ketones or aldehydes are smoothly deprotected in neutral conditions by irradiation with 350 nm light. The chemical stability in basic, acidic, and oxidizing media makes this form of protection orthogonal to classical protecting groups. Both racemic and enantiopure forms are readily available in two steps from inexpensive starting materials.
Solid–Electrolyte Interphase Formation and Electrolyte Reduction at Li-Ion Battery Graphite Anodes: Insights from First-Principles Molecular Dynamics (2012)

Understanding the nature and formation of the solid–electrolyte interphase (SEI) formed in electrochemical storage devices, such as Li-ion batteries, is most important for improving functionality. Few experiments exist that adequately probe the SEI, particularly in situ. We perform predictive ab initio molecular dynamics simulations of the anode–electrolyte interface for several electrolytes and interface functionalizations. These show strongly differing effects on the reducibility of the electrolyte. Electrolyte reduction occurs rapidly, on a picosecond time scale. Orientational ordering of electrolyte near the interface precedes reduction. The reduced species depend strongly on surface functionalization and presence of LiPF6 salt. While LiPF6 salt in ethylene carbonate is more stable at a hydrogen-terminated anode, oxygen/hydroxyl termination causes spontaneous dissociation to form LiF and other fluorophosphates. LiF migrates to the interface creating chainlike structures, consistent with experimental observations of LiF agglomeration. Inorganic products such as LiF and Li2CO3 migrate closer to the anode than purely organic components, consistent with their more ionic character. Significantly, we conclude that while the electrolyte reduction occurs at the molecular level near the interface, requiring specific alignments and proximity, the reducibility is governed by the average reduction potential barrier between the electrode (anode) and the electrolyte.
Non‐invasive in vivo determination of UVA efficacy of sunscreens using diffuse reflectance spectroscopy (2003)

This study showed that DRS is a rapid and reproducible method to calculate UVA efficacy of sunscreen materials and that its results correlate closely with those obtained by human phototesting.
Reactions of the anion of quinazoline Reissert compound (3-benzoyl-3,4-dihydro-4-quinazolinecarbonitrile) with electrophiles. (1985)

Reactions of the quinazoline Reissert compound (2) with various electrophiles in the presence of sodium hydride in N, N-dimethylformamide were investigated. The reactions with aldehydes (3) and ketones (12) gave α-aryl (or alkyl)-(7) and α-alkyl-α-aryl (or alkyl)-4-quinazolinylmethyl benzoates (16), respectively. The reaction with π-deficient heteroaromatics (10a-c) gave 4-heteroarylquinazolines (20a-c). Alkylation (or arylation) with alkyl (or aryl) halides (23a-c) afforded 4-substituted 3-benzoyl-3, 4-dihydro-4-quinazolinecarbonitriles (24a-c). The reaction with dimethyl acetylenedicarboxylate proceeded in two ways, giving dimethyl 3-phenylpyrrolo [1, 2-c] quinazoline-1, 2-dicarboxylate (27) and dimethyl 3-benzoyl-4-cyano-1, 2, 3, 4-tetrahydro-2, 4-ethenoquinazoline-9, 10-dicarboxylate (28). The reaction with 2-alkenonitriles (29a, b) resulted in the formation of 2-benzoyl-3-(4-quinanolinyl) alkanonitriles (32a, b).
Role of RyR2 Phosphorylation in Heart Failure and Arrhythmias (2014)

This Controversies in Research article discusses the hypothesis that protein kinase A (PKA)-mediated phosphorylation of the Ryanodine Receptor (RyR) at a single serine (RyRS2808) is essential for normal sympathetic regulation of cardiac myocyte contractility and is responsible for the disturbed Ca(2+) regulation that underlies depressed contractility in heart failure. Studies supporting this hypothesis have associated hyperphosphorylation of RyRS2808 and heart failure progression in animals and humans and have shown that a phosphorylation defective RyR mutant mouse (RyRS2808A) does not respond normally to sympathetic agonists and does not exhibit heart failure symptoms after myocardial infarction. Studies to confirm and extend these ideas have failed to support the original data. Experiments from many different laboratories have convincingly shown that PKA-mediated RyRS2808 phosphorylation does not play any significant role in the normal sympathetic regulation of sarcoplasmic reticulum Ca2+ release or cardiac contractility. Hearts and myocytes from RyRS2808A mice have been shown to respond normally to sympathetic agonists, and to increase Ca(2+) influx, Ca(2+) transients, and Ca(2+) efflux. Although the RyR is involved in heart failure-related Ca(2+) disturbances, this results from Ca(2+)-calmodulin kinase II and reactive oxygen species-mediated regulation rather than by RyR2808 phosphorylation. Also, a new study has shown that RyRS2808A mice are not protected from myocardial infarction. Collectively, there is now a clear consensus in the published literature showing that dysregulated RyRs contribute to the altered Ca(2+) regulatory phenotype of the failing heart, but PKA-mediated phosphorylation of RyRS2808 has little or no role in these alterations.
Improving the efficacy of antibody-interleukin 2 fusion proteins by reducing their interaction with Fc receptors. (1999)

Fusion proteins between whole antibodies (Abs) and cytokines (immunocytokines) such as interleukin 2 have shown efficacy in several mouse tumor models despite a circulating half-life that is significantly shorter than that of the original Ab. We have examined the potential mechanisms responsible for clearance and shown that an important factor is enhanced binding to Fc receptor (FcR). Improvements in the half-lives of two different immunocytokines were made by changing the isotype of the human heavy chain C region from IgG1 or IgG3 to those with reduced binding to FcR, e.g., IgG4. The same effect could also be achieved through site-directed mutagenesis of the FcR binding site in the IgG1 H chain. In vitro studies using mouse J774 FcR-expressing cells showed increased binding of interleukin 2-based immunocytokines, relative to their corresponding Abs, and that this was reversed in those fusion proteins made with IgG4 or mutated IgG1 H chains. All of the fusion proteins showing reduced FcR binding also had reduced Ab-dependent cellular cytotoxicity activity, as measured in 4-h chromium release assays. A complete loss of complement-dependent cytotoxicity activity was seen with an IgG4-based immunocytokine derived from an IgG1 Ab with potent activity. Despite these reduced effector functions, the IgG4-based immunocytokines with extended circulating half-lives showed equivalent (in the case of severe combined immunodeficiency mouse xenograft models) or better (in the case of syngeneic models) efficacy in mouse tumor models than the original IgG1-based molecules. These novel immunocytokines may show improved efficacy in therapeutic situations where T cell- rather than natural killer- or complement-mediated antitumor mechanisms are involved.