gebhart/patrepeval huggingface dataset:
Adverse Effects of Antiretroviral Drugs on HIV-1-Infected and -Uninfected Human Monocyte-Derived Macrophages (2006)

Antiretroviral drugs approved for treatment of HIV-1 infection include nucleoside reverse transcriptase inhibitors (NRTIs) and protease inhibitors (PIs). Use of these drugs in combinations (highly active antiretroviral therapy) has delayed disease progression. However, long-term therapy is associated with potentially serious adverse effects. NRTIs are thought to contribute to these adverse effects via depletion of mtDNA. Inasmuch as macrophages (major targets for HIV-1) are highly metabolically active with large numbers of mitochondria, we investigated the effects of NRTIs (didanosine, stavudine, lamivudine, and zidovudine) on the viability and function of HIV-1-infected and -uninfected human monocyte-derived macrophages (MDMs). We demonstrate that the combinations didanosine/stavudine and lamivudine/zidovudine decrease mtDNA content in MDMs, with HIV-1-infected MDMs displaying a greater reduction than uninfected cells. This decrease correlated with decreased complement-mediated phagocytosis (C'MP) by MDMs, a process dependent on mitochondrial function. Inasmuch as PIs have previously been reported to interact with cellular proteases and given that cellular proteases are involved in the phagocytic process, we investigated the effects of the PI indinavir on C'MP. We demonstrate that indinavir augments C'MP by uninfected MDMs, but not HIV-1-infected MDMs. This study provides additional understanding on the effects of commonly used antiretroviral drugs on cellular immune function.
Phase I study of highly selective inhibitor of VEGFR tyrosine kinase, tivozanib, in Japanese patients with solid tumors (2013)

Tivozanib is a potent and selective inhibitor of vascular endothelial growth factor receptor (VEGFR) tyrosine kinases. A previous clinical trial in the EU and USA indicated that tivozanib at the maximum tolerated dose of 1.5 mg/day showed an antitumor activity in patients with renal cell carcinoma. This Japanese phase I study was designed to determine the recommended phase II dose of tivozanib for Japanese patients; secondary objectives included pharmacokinetic/pharmacodynamic profiles and preliminary efficacy. Daily treatment with tivozanib in a 3-weeks-on/1-week-off cycle was examined in nine Japanese patients with advanced solid tumors in the 3 + 3 design (Level 1, 1.0 mg; Level 2, 1.5 mg). No dose-limiting toxicity was observed throughout the study, and the maximum tolerated dose was not reached. The most commonly observed drug-related adverse events were diarrhea, dysphonia, rash, thyroid stimulating hormone increase, and with severity grade ≥3, hand-foot skin reaction, hypertension, and proteinuria. Those adverse events were generally well-manageable and mostly resolved within the tolerability evaluation period. Serum exposure to tivozanib resulted in t1/2 of more than >60 h. Increase of plasma VEGF and decrease of plasma VEGFR-1 and VEGFR-2 were observed 1-3 weeks after tivozanib treatment. Although no complete or partial response was observed, long-term stable disease continuing more than 170 days was observed in three renal cell carcinoma patients who had failed prior VEGFR inhibitors. In conclusion, 1.5 mg/day of tivozanib in a 3-weeks-on/1-week-off setting was tolerable in Japanese patients, and was recommended for further clinical trials in the Japanese population. Clinical trial Registration No: JapicCTI-090854.
Hydroxide-induced synthesis of the superoxide ion from dioxygen and aniline, hydroxylamine, or hydrazine (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydroxide-induced synthesis of the superoxide ion from dioxygen and aniline, hydroxylamine, or hydrazineSeungwon Jeon and Donald T. SawyerCite this: Inorg. Chem. 1990, 29, 23, 4612–4615Publication Date (Print):November 1, 1990Publication History Published online1 May 2002Published inissue 1 November 1990https://pubs.acs.org/doi/10.1021/ic00348a007https://doi.org/10.1021/ic00348a007research-articleACS PublicationsRequest reuse permissionsArticle Views191Altmetric-Citations9LEARN 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
Comparison of Bottom-Up and Top-Down Procedures for Water Demand Reconstruction (2020)

This paper presents a comparison between two procedures for the generation of water demand time series at both single user and nodal scales, a top-down and a bottom-up procedure respectively. Both procedures are made up of two phases. The top-down procedure adopted includes a non-parametric disaggregation based on the K-nearest neighbours approach. Therefore, once the temporal aggregated water demand patterns have been defined (first phase), the disaggregation is used to generate water demand time series at lower levels of spatial aggregation (second phase). In the bottom-up procedure adopted, demand time series for each user and for each time step are generated applying a beta probability distribution with tunable bounds or a gamma distribution with shift parameter (first phase). Then, a Copula based re-sort is applied to the demand time series generated to impose existing rank cross-correlations between users and at all temporal lags (second phase). For the sake of comparison, two case studies were considered, both of which are related to a smart water network in Naples (Italy). The results obtained show that the bottom-up procedure performs significantly better than the top-down procedure in terms of rank-cross correlations at fine scale. However, the top-down procedure showed a better performance in terms of skewness and rank cross-correlation when the aggregated demands were considered. Finally, the level of aggregation in nodes was found to affect the performance of both the procedures considered.
Structural and Cognitive Bottlenecks to Information Access in Social Networks (2013)

Information in networks is non-uniformly distributed, enabling individuals in certain network positions to get preferential access to information. Social scientists have developed influential theories about the role of network structure in information access. These theories were validated through numerous studies, which examined how individuals leverage their social networks for competitive advantage, such as a new job or higher compensation. It is not clear how these theories generalize to online networks, which differ from real-world social networks in important respects, including asymmetry of social links. We address this problem by analyzing how users of the social news aggregator Digg adopt stories recommended by friends, i.e., users they follow. We measure the impact different factors, such as network position and activity rate; have on access to novel information, which in Digg's case means set of distinct news stories. We show that a user can improve his information access by linking to active users, though this becomes less effective as the number of friends, or their activity, grows due to structural network constraints. These constraints arise because users in structurally diverse position within the follower graph have topically diverse interests from their friends. Moreover, though in most cases user's friends are exposed to almost all the information available in the network, after they make their recommendations, the user sees only a small fraction of the available information. Our study suggests that cognitive and structural bottlenecks limit access to novel information in online social networks.
Using Program Analysis to Improve Database Applications. (2014)

Applications that interact with database management systems (DBMSs) are ubiquitous. Such database applications are usually hosted on an application server and perform many small accesses over the network to a DBMS hosted on the database server to retrieve data for processing. For decades, the database and programming systems research communities have worked on optimizing such applications from different perspectives: database researchers have built highly efficient DBMSs, and programming systems researchers have developed specialized compilers and runtime systems for hosting applications. However, there has been relatively little work that optimizes database applications by considering these specialized systems in combination and looking for optimization opportunities that span across them. In this article, we highlight three projects that optimize database applications by looking at both the programming system and the DBMS in a holistic manner. By carefully revisiting the interface between the DBMS and the application, and by applying a mix of declarative database optimization and modern program analysis techniques, we show that a speedup of multiple orders of magnitude is possible in real-world applications.
Optical dosimetry in photodynamic therapy (1986)

The diffusion approximation for the radiant flux distribution in a tissue layer has been applied to optical dosimetry in photodynamic therapy of malignant tumors. The model assumes that tumor eradication requires a minimum absorbed energy by the localized photosensitizer, taken as 0.19 J/cm3 for hematoporphyrin derivative (HPD) at 630 nm. The analysis leads to the required incident irradiance for front surface illumination as a function of the tumor depth, the optical penetration depth of the tumor, and the concentration of localized sensitizer. The effect of HPD photobleaching on the required light dose and drug dose levels is considered. The results are given in tabular form for typical clinical applications.
THE STRUCTURE OF NORMAL SMALL LYMPHATICS (1961)

The structure of the lymphatic capillaries and lacunes as seen by electron microscopy was similar to that of the blood capillaries of, for instance, skeletal muscle. All the lymphatic endothelial cells contained many vesicles and caveolæ intercellulares. No fenestrations in the endothelium were seen, but some intercellular junctions were patent, especially in diaphragmatic lacunes. The basement membrane was less regular than that of blood capillaries or of mesothelium and in many places, especially in diaphragmatic lacunes, it appeared to be absent. Carbon and ferritin were injected into the peritoneal cavity and could be seen in the lumen of diaphragmatic lacunes, in vesicles in mesothelium and endothelium, and in patent junctions between endothelial cells. Deposits of ferritin without an encircling membrane were also seen in the cytoplasm.
Standard handbook of machine design (1997)

Introductions: Standards, Codes, Regulations. Statistical Considerations. Measurement and Inference Numerical Methods. Computational Considerations. Wear. Solid Materials. The Strength of Cold-Worked and Heat-Treated Steels. Usability. Safety. Minimizing Engineering Effort. Strength Under Static Circumstances. Fundamentals of Arc Welding. Instabilities in Beams and Columns. Curved Beams and Rings. Seals. Flywheels. Limits and Fits. Power Screws. Threaded Fasteners. Unthreaded Fasteners. Bolted and Riveted Joints. Springs. Lubrication. Gaskets. Rolling-Contact Bearings. Journal Bearings. Couplings. Clutches and Brakes. Belt Drives. Chain Drives. Spur Gears. Bevel and Hypoid Gears. Helical Gears. Worm Gearing. Shafts. Vibration and Control of Vibration. A Thesaurus of Mechanisms. Cam Mechanisms. Linkages. Load-Cycle Analysis. Fluid Power Systems and Circuit Design. Corrosion. Noise and Its Control. Gear Trains. Robots and Smart Machines. Sections and Shapes-Tabular Data. Stress. Deflection.
Oligonucleotides Containing 7-Deaza-2′-deoxyxanthosine: Synthesis, Base Protection, and Base-Pair Stability (2006)

Oligonucleotides incorporating 7-deaza-2′-deoxyxanthosine (3) and 2′-deoxyxanthosine (1) were prepared by solid-phase synthesis using the phosphoramidites 6–9 and 16 which were protected with allyl, diphenylcarbamoyl, or 2-(4-nitrophenyl)ethyl groups. Among the various groups, only the 2-(4-nitrophenyl)ethyl group was applicable to 7-deazaxanthine protection being removed with 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) by β-elimination, while the deprotection of the allyl residue with Pd0 catalyst or the diphenylcarbamoyl group with ammonia failed. Contrarily, the allyl group was found to be an excellent protecting group for 2′-deoxyxanthosine (1). The base pairing of nucleoside 3 with the four canonical DNA constituents as well as with 3-bromo-1-(2-deoxy-β-D-erythro-pentofuranosyl)-1H-pyrazolo[3,4-d]pyrimidine-4,6-diamine (4) within the 12-mer duplexes was studied, showing that 7-deaza-2′-deoxyxanthosine (3) has the same universal base-pairing properties as 2′-deoxyxanthosine (1). Contrary to the latter, it is extremely stable at the N-glycosylic bond, while compound 1 is easily hydrolyzed under slightly acidic conditions. Due to the pKa values 5.7 (1) and 6.7 (3), both compounds form monoanions under neutral conditions (95% for 1; 65% for 3). Although both compounds form monoanions at pH 7.0, pH-dependent Tm measurements showed that the base-pair stability of 7-deaza-2′-deoxyxanthosine (3) with dT is pH-independent. This indicates that the 2-oxo group is not involved in base-pair formation.
Theoretical formalism for collective spin-wave edge excitations in arrays of dipolarly interacting magnetic nanodots (2016)

A general theory of collective spin-wave edge modes in semi-infinite and finite periodic arrays of magnetic nanodots having uniform dynamic magnetization (macrospin approximation) is developed. The theory is formulated using a formalism of multivectors of magnetization dynamics, which allows one to study edge modes in arrays having arbitrarily complex primitive cells and lattice structure. The developed formalism can describe spin-wave edge modes localized both at the physical edges of the array and at the internal ``domain walls'' separating the array regions existing in different static magnetization states. Using a perturbation theory, in the framework of the developed formalism, it is possible to calculate damping of the edge modes and to describe their excitation by external variable magnetic fields. The theory is illustrated on the following practically important examples: (i) calculation of the FMR absorption in a finite nanodot array having the shape of a right triangle; (ii) calculation of the spectra of nonreciprocal spin-wave edge modes, including the modes at the physical edges of an array and modes at the domain walls inside the array; and (iii) study of the influence of the domain wall modes on the FMR spectrum of an array existing in a nonideal chessboard antiferromagnetic ground state.
Reflections of the founding Chair (2011)

This article looks back at the inception of the Association of Commonwealth Universities PR, Marketing and Communciations Network in 2003, of which the author was the founding Chair. It considers the changes that had taken place since the Network was founded and offers some views on the future.
Preparation of Tetrahydroisoquinoline‐3‐ones Via Cyclization of Phenyl Acetamides Using Eaton's Reagent (2014)

Abstract Chlorophenylacetic acid Thionyl chloride Methylamine 2‐(4‐chlorophenyl)‐ N ‐ Methylacetamide Eaton's reagent Paraformaldehyde
Orally administered immunosuppressants modify intestinal uptake of nutrients in rabbits. (1994)

The effect on intestinal nutrient transport of the immunosuppressive drugs cyclosporin A (CsA), cyclosporin G (CsG), and rapamycin (RAP) was determined in New Zealand white rabbits. Rabbits received oral doses of CsA (20 mg/kg/day), CsG (10 mg/kg/day), or RAP (1 mg/kg/day) for 10 days. Animals receiving RAP had decreased food intake and weight gain compared with controls. This correlated with a decrease in both total ileal weight and corresponding mucosal weight. CsA and CsG administration had no effect on food intake, total weight gain, or intestinal weight. Villus surface area was significantly decreased in all groups as compared with controls. Jejunal uptake of D-glucose as well as 1 medium and 4 long chain fatty acids was not affected by drug administration, while both mucosal-to-serosal and net 3-0-methylglucose fluxes were increased (P < 0.05) in the jejunum by all 3 drugs. In the ileum, the rates of uptake of D-glucose as well as stearic and linoleic acids were increased in animals treated with RAP compared with controls. There was an increase in the ileal values of the maximal transport rate (Vmax) and apparent Michaelis constant (Km*) in RAP, and a fall in the Vmax and Km* in CsG. CsG administration resulted in a decreased cholesterol uptake in both jejunum and ileum, and a decreased D-glucose uptake in the ileum compared with controls. These differences in glucose uptake among groups could not be attributed to variations in body, intestinal, or mucosal weights. It is unlikely that the changes observed in CsA- and CsG-treated animals would have nutritional importance, as these animals gained weight normally. In addition, in these animals the changes mainly occurred in the ileum, not in the jejunum, where most glucose is absorbed, and the associated alterations in the values of the Vmax and Km* would lead to reciprocal changes in the rates of uptake of varying luminal concentrations of glucose. In contrast, these changes are likely to be of more importance in RAP-treated animals, since they failed to gain weight normally. The significance of these findings needs to be established in chronically treated animals.
Pilot study of PET imaging of 124I-iodoazomycin galactopyranoside (IAZGP), a putative hypoxia imaging agent, in patients with colorectal cancer and head and neck cancer (2013)

ClinicalTrials.gov NCT00588276.
Anaplastic lymphoma kinase (ALK): A potential oncogenic driver in triple-negative breast cancer? (2013)

1067 Background: TNBC, a molecularly heterogeneous subset of breast cancer, has an aggressive clinical course and no established targets for therapy. Wild-type ALK gene amplification by fluorescence in situ hybridization (FISH) was noted in 6/9 inflammatory TNBC specimens (Robertson et al. SABCS, P3-01-18). The status of ALK, full-length or fused, in non-inflammatory TNBC has not been described. Identification of a biomarker such as ALK in TNBC would be clinically significant, given the ongoing development of multiple ALK inhibitors. We screened for ALK expression in TNBC specimens with a novel patented qRT-PCR assay (Insight ALK Screen). Methods: We tested archived formalin-fixed, paraffin-embedded blocks of TNBC tissue. Evaluable specimens had sufficient tumor material for 10 slides with 5-micron sections. Insight ALK Screen was performed using previously described methodology (Hout, et al. AACR 2011, Abstract 2220). We subjected ALK Screen positive specimens to ALK break-apart FISH (Vysis ) and direct sequencing analysis. Results: See clinical characteristics (Table). Insufficient RNA: 8/40 (20%). Insight ALK Screen-positive: 8/32 (25%). Break-apart FISH performed on these 8 specimens suggested 3/8 to be positive for ALK translocation and 2/8 to contain amplification of ALK without a translocation. The ALK-amplified specimens were subsequently confirmed with sequencing of RNA-PCR products to express full-length ALK. One additional ALK Screen-positive, FISH-negative specimen had full-length ALK expression confirmed on sequencing. Further analysis of the other 2 ALK Screen-positive cases is pending. Conclusions: ALK expression was seen in ~25% of TNBC specimens screened by Insight ALK Screen. We observed both ALK translocations and amplification/overexpression of full-length ALK. We are testing additional specimens by FISH and immunohistochemistry to evaluate the full spectrum of ALK alterations in TNBC. Updated data will be presented. [Table: see text]
Short Communication Seventeen polymorphic microsatellite markers developed for the Javelin goby, Synechogobius hasta (Gobiidae) (2012)

Synechogobius hasta is an important commercial marine fish with distinctive features of rapid growth and short lifespan. We isolated and characterized 17 microsatellite markers for S. hasta using a (GT)(13)-enriched genomic library. Polymorphism was assessed in 48 individuals from a single population collected from the northern coastal waters of the Yellow Sea. The number of alleles per locus ranged from 2 to 23, with a mean of 11.3. The observed and expected heterozygosities ranged from 0.130 to 1.000 and from 0.123 to 0.939, with means of 0.758 and 0.774, respectively. Fourteen of 17 loci conformed to Hardy-Weinberg equilibrium and no significant linkage disequilibrium between locus pairs was detected. These microsatellite markers will be useful for population genetic structure analyses.
Prediction of Low-Energy Collision-Induced Dissociation Spectra of Peptides (2004)

A kinetic model, based on the "mobile proton" model of peptide fragmentation, was developed to quantitatively simulate the low-energy collision-induced dissociation (CID) spectra of peptides dissociated in a quadrupole ion trap mass spectrometer. The model includes most fragmentation pathways described in the literature, plus some additional pathways based on the author's observations. The model was trained by optimizing parameters within the model for predictions of CID spectra of known peptides. A best set of parameters was optimized to obtain best match between the simulated spectra and the experimental spectra in a training data set. The performance of the mathematical model and the associated optimized parameter set used in the CID spectra simulation was evaluated by generating predictions for a large number of known peptides, which were not included in the training data set. It was shown that the model is able to predict peptide CID spectra with reasonable accuracy in fragment ion intensities for both singly and doubly charged peptide parent ions up to 2000 u in mass. The optimized parameter set was evaluated to gain insight into the collision-induced peptide fragmentation process.
6-Dialkylaminobenzimidazole Nonlinear Optical Dyes (2012)

Abstract A new 6-dialkylaminobenzimidazole nonlinear optical dye was synthesized in eight linear steps with an overall yield of 16%.